Structure and Regulation of Soluble Guanylate Cyclase

Home , Guanylate cyclase, Nitric oxide synthase, Nitrosation, Soluble guanylyl cyclase

BI81CH22-Marletta ARI 3 May 2012 12:17

Emily R. Derbyshire1 and Michael A. Marletta2

1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115 2Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037; email: [email protected]

Annu. Rev. Biochem. 2012. 81:533–59 Keywords First published online as a Review in Advance on nitric oxide, heme, signaling, desensitization, nitrosation February 9, 2012 The Annual Review of Biochemistry is online at Abstract biochem.annualreviews.org Nitric oxide (NO) is an essential signaling molecule in biological sys- This article’s doi: tems. In mammals, the diatomic gas is critical to the cyclic guano- 10.1146/annurev-biochem-050410-100030 sine monophosphate (cGMP) pathway as it functions as the primary Copyright c 2012 by Annual Reviews. activator of soluble guanylate cyclase (sGC). NO is synthesized from All rights reserved L-arginine and oxygen (O2) by the enzyme nitric oxide synthase (NOS). 0066-4154/12/0707-0533$20.00

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org Once produced, NO rapidly diffuses across cell membranes and binds to the heme cofactor of sGC. sGC forms a stable complex with NO

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. and carbon monoxide (CO), but not with O2. The binding of NO to sGC leads to signiﬁcant increases in cGMP levels. The second mes- senger then directly modulates phosphodiesterases (PDEs), ion-gated channels, or cGMP-dependent protein kinases to regulate physiological functions, including vasodilation, platelet aggregation, and neurotransmission. Many studies are focused on elucidating the molecular mechanism of sGC activation and deactivation with a goal of therapeutic intervention in diseases involving the NO/cGMP-signaling pathway. This review summarizes the current understanding of sGC structure and regulation as well as recent developments in NO signaling.

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INTRODUCTION Contents The nitric oxide/cyclic guanosine monophos- INTRODUCTION...... 534 phate (NO/cGMP) pathway was discovered Enzymes Critical to the Nitric in the 1980s, but chemical modulation of the Oxide/Cyclic Guanosine pathway for the treatment of angina pectoris Monophosphate Pathway...... 534 had been unknowingly achieved 100 years ISOLATION OF SOLUBLE earlier. This stimulation of cGMP production GUANYLATE CYCLASE ...... 535 occurred with the clinical administration of SOLUBLE GUANYLATE organic nitrites (isoamyl nitrite) (1) and organic CYCLASEISOFORMS...... 537 nitrates (glyceryl trinitrate; GTN) (2). These ARCHITECTURE OF SOLUBLE compounds alleviate the pain associated with GUANYLATE CYCLASE ...... 538 angina by relaxing the vascular smooth muscle, Heme-Nitric Oxide and Oxygen leading to vasodilation. For years, investiga- BindingDomain...... 538 tions were focused on the mechanism of smooth Per/Arnt/Sim and Coiled-Coil muscle relaxation by these molecules, and these Domains...... 539 efforts led to the discovery that NO is a physio- CatalyticDomain...... 539 logically relevant signaling molecule. Addition- SOLUBLE GUANYLATE ally, these efforts led to the identification of the CYCLASE HOMOLOGS ...... 540 enzymes that biosynthesize NO and cGMP. Eukaryotic Atypical Soluble GuanylateCyclases...... 540 Enzymes Critical to the Nitric Prokaryotic Heme-Nitric Oxide Oxide/Cyclic Guanosine and Oxygen Binding Monophosphate Pathway Proteins...... 541 STRUCTURAL INSIGHTS FROM Early studies showed that both cytosolic and STUDIES ON SOLUBLE particulate fractions of mammalian tissue GUANYLATE CYCLASE AND exhibit guanylate cyclase activity. Within ITSHOMOLOGS...... 542 the insoluble fractions, membrane-bound LIGANDSELECTIVITY...... 545 particulate guanylate cyclases are present, REGULATION OF SOLUBLE which are activated by natriuretic peptides GUANYLATE CYCLASE BY (reviewed in References 3 and 4), whereas the NITRICOXIDE...... 546 cytosolic fractions contain soluble guanylate Activation and Nitric Oxide cyclases (sGCs), which are activated by NO. Association...... 546 NO-responsive guanylate cyclase activity is Deactivation and Nitric Oxide also associated with cell membranes in certain Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org Dissociation...... 547 tissues, including skeletal muscle and brain, as Desensitization...... 548 well as in platelets (5–7). Guanylate cyclases Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. MODULATORS OF SOLUBLE are found in most tissues, and the distribution GUANYLATE CYCLASE of these proteins in various cells is isoform ACTIVITY...... 549 specific. This provides an additional means to Soluble Guanylate Cyclase regulate cGMP-dependent responses because Activators...... 549 localized pools of the signaling molecule can Soluble Guanylate Cyclase be generated within specific tissues and in Inhibitors...... 550 proximity to either soluble or membrane- bound cGMP receptors. Thus, tissues can

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regulate cGMP levels by expression of specific phosphodiesterases (PDEs), ion-gated chan- cGMP: cyclic GC isoforms, and the isoforms have a distinct nels, and cGMP-dependent protein kinases guanosine peptide receptor or ligand activator. Addi- in the regulation of several physiological monophosphate tionally, a reciprocal communication between functions, including vasodilation, platelet GTN: glyceryl particulate guanylate cyclase and sGC has been aggregation, and neurotransmission (9–11). trinitrate observed in the regulation of human and mouse In 1998, the Nobel Prize in Physiology or Vasodilation: blood vascular homeostasis (8), and it remains likely Medicine was awarded to Robert F. Furchgott, vessel widening from that communication between these pathways Louis J. Ignarro, and Ferid Murad, in recogni- smooth muscle occurs in several cGMP-dependent processes. tion of their achievements toward the discovery relaxation Generally, in eukaryotic NO signaling, of the NO-signaling pathway. Currently, this sGC: soluble the initial event involves calcium release, pathway is actively studied because drugs mod- guanylate cyclase followed by binding of a calcium/calmodulin ulating NO-dependent processes have the po- NOS: nitric oxide complex to nitric oxide synthase (NOS), which tential to treat several maladies, including car- synthase activates the enzyme. NO is synthesized and diovascular and neurodegenerative diseases, as then diffuses into target cells, where it binds well as various airway diseases. to the heme in sGC (Figure 1). sGC is a histidine-ligated hemoprotein that binds NO and carbon monoxide (CO), but not oxygen ISOLATION OF SOLUBLE GUANYLATE CYCLASE (O2). This binding event leads to a several hundredfold increase in cGMP synthe- Despite many years of research on sGC, an ef- sis. Once formed, cGMP targets include ficient low-cost purification of the protein has

Generator ccellell Ta Target cell

2+ α1 β1 Ca /CaM GTP NO L-Arg + O2 FeII Mg2+

sGC cGMP + PPi NOS L-Cit + NO cGK cGMP-gated Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org PDE ion channels Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only.

Figure 1 The nitric oxide/cyclic GMP (NO/cGMP)-signaling pathway. A Ca2+/calmodulin (CaM) complex binds nitric oxide synthase (NOS). NOS catalyzes the oxidation of L-arginine (L-Arg) to L-citrulline (L-Cit) and nitric oxide (NO). NO binds to the FeII heme of α1β1 soluble guanylate cyclase (sGC) at a diffusion- controlled rate. This binding event leads to signiﬁcant increases in cGMP and pyrophosphate (PPi). cGMP then binds to and activates cGMP-dependent protein kinases (cGKs), phosphodiesterases (PDEs) and ion-gated channels. Abbreviations: α1andβ1, soluble guanylate cyclase subunits; CaM, calmodulin.

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remained elusive, but several methods have sGC. A clear advantage of the Sf9/baculovirus been developed that yield low microgram expression system is that it enables in vitro amounts of homogeneous protein. Initial char- characterization, including the generation GTP: guanosine 5-triphosphate acterization of sGC was carried out with pro- of site-directed mutants. However, both the tein obtained from rat and bovine tissues. By COS-7 and Sf9/baculovirus expression systems the 1980s, studies were being done with pu- facilitated the biochemical characterization of rified sGC from rat lung (12) and liver (13), subunit dimerization, allowed for the gener- as well as from bovine lung (14, 15); these ation of site-directed mutants, and provided studies showed sGC to be a heterodimer. Im- larger quantities of enzyme for in vitro studies. portantly, it was observed that sGC could be The full-length mammalian α1β1het- purified with and without the heme cofac- erodimer has not yet been isolated from a bac- tor, depending on the purification protocol. terial expression system, but several truncations In short, the use of solubilizing agents or am- of sGC have been successfully obtained via ex- monium sulfate precipitation can lead to mis- pression in Escherichia coli. These proteins in- folded apoprotein. Heme reconstitution of this clude N-terminal truncations of α1, β1, and apoprotein yields an sGC species [later termed β2 (28–30), C-terminal truncations of α1and sGC1 by Vogel et al. (16)] with biochemi- β1 (31, 32), and a domain within the central re- cal properties that vary from the native pro- gion of β1(Figure 2) (31). These constructs tein [named sGC2 by Vogel et al. (16)]. To purify with yields ranging from 0.5 to 5 mg date, the bovine lung sGC prep is the most ef- ficient method of isolating heme-bound pro- a Domain architecture of sGC tein from source tissue (17, 18). This method typically yields ∼1 mg of pure protein per α

kilogram of lung. Heme The development of heterologous expres- β sion systems for recombinant sGC expression H-NOX PAS CC CAT led to significant advances. The first successful heterologous expression system for sGC was b Characterized sGC truncations accomplished in COS-7 cells (19). Although COS-7 cells do not produce enough sGC for Heme binding protein purification, the procedure was pivotal β1(1–385) to establishing that sGC is an obligate heterodimer composed of α1andβ1 subunits (20). β1(1–194) Additionally, COS-7 cells have been used to β2(1–217) examine mutants and truncations of sGC via

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org lysate activity assays (21, 22). GTP binding The overexpression of rat sGC in insect cells α1(467–690)

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. with the Sf9/baculovirus expression system was

the first procedure used to isolate pure recom- β1(414–619) binant protein (21, 23, 24). sGC expression in insect cells was initially accomplished without Figure 2 an affinity tag (21), but current protocols Domain architecture of soluble guanylate cyclase involve a His tag to facilitate the purification (sGC). (a) Heme-nitric oxide/oxygen binding process (25–27). Although highly expressed, (H-NOX, yellow), Per/Arnt/Sim domain (PAS, gray), coiled-coil domains (CC, white), and catalytic most (>90%) of the protein is insoluble. This domains (CAT, blue)areshown.(b) Characterized method typically yields 0.2–0.4 mg of pure sol- heme-binding and GTP-binding truncations of rat uble protein per liter of culture and is now com- sGC. Heme is represented by the red parallelogram. monly used to obtain purified rat and human α1, β1, and β2 isoforms are shown.

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of pure protein per liter of culture. Recently a dominant-negative protein (39). Despite the an E. coli expression system was used for the similar biochemical properties of the two phys- full-length Manduca sexta α1β1 heterodimer iologically relevant sGC heterodimers, they (33). This method provides low amounts (0.5– have unique roles in cGMP signaling that may 1 mg/liter) of partially pure full-length protein, be attributed to their varying cellular local- but higher yields (1–2 mg/liter) of pure protein ization. Specifically, α2β1 has been associated were obtained by truncating the C terminus of with the membrane in several tissues (5–7), the α1andβ1 subunits (33). The resulting het- and consequently, α2β1 responds differently erodimeric proteins (msGC-NT1 and msGC- than cytosolic α1β1 (37). In rat brain, it was NT2) lack the ability to cyclize GTP but can be found that this association is mediated by an purified to homogeneity. Perhaps future work interaction between the C terminus of the α2 optimizing the expression conditions and/or protein and PSD-95 (postsynaptic density-95) purification of sGC from E. coli will overcome protein (6). Most recently, a distinct presy- the current limitations in protein yield. naptic role has been identified for α1β1in glutamate release in the hippocampus (40). The β2 isoform is not ubiquitously ex- SOLUBLE GUANYLATE pressed like the β1 isoform, and analysis of CYCLASE ISOFORMS mRNA levels indicates that it is found primarily Heterodimeric sGC consists of two homolo- in the kidney (35). Unlike β1, the C terminus gous subunits, α and β. The most commonly of β2 contains a possible isoprenylation site, studied isoform is the α1β1 protein; however, but the subcellular localization of this protein α2andβ2 subunits have also been identified is unknown. The β2 isoform has not yet been (34, 35). These proteins were first character- purified and characterized, but the protein has ized in mammals, but they also exist in insects, been studied after transient expression in insect such as Drosophila melanogaster and M. sexta,and cells. Using this approach, it was found that β2 in fish. Isoforms of α-subunits are highly ho- does not exhibit cyclase activity when expressed mologous with ∼48% sequence identity, and with α1orα2 but that β2 is active in the absence β-subunits have an overall sequence identity of of an α-subunit, suggesting that the β2protein ∼41%. can function as a homodimer ex vivo (41). This The localization of each subunit has been is in contrast to the β1 protein, which has been studied in mammals, including humans, rats, isolated as an inactive homodimer after overex- and cows. Both α1andβ1 subunits are expression in insect cells (26). In rat kidney, the pressed in most tissues, and it is well accepted mRNA levels of the β2 subunit were shown to that these proteins form a physiologically be developmentally regulated (42); however, it relevant heterodimer (36). By quantitative remains unclear what the physiological role of

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org polymerase chain reaction analysis and West- the β2 isoform is in cGMP signaling. ern blotting, the α2 subunit is found in fewer Recently, several genetic studies in mouse

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. tissues when compared to the α1andβ1iso- models have emphasized the importance of forms but is highly expressed in the brain, lung, the various sGC isoforms for physiological colon, heart, spleen, uterus, and placenta (36). processes (reviewed in Reference 43). Knock- Studies with puriﬁed protein have shown that out mice lacking the sGC β1 subunit exhibit the α2β1 heterodimer exhibits ligand-binding elevated blood pressure, reduced heart rate, characteristics identical to the α1β1het- and dysfunction in gastrointestinal contractility erodimer (37, 38), but a splice variant of the α2 (44). Additionally, deletion of the β1 subunit subunit (α2i) forms a dimer with the β1 subunit within only smooth muscle cells implicates the to form an inactive complex. α2i contains an loss of the protein in these cells as the cause in-frame insertion of 31 amino acids within of hypertension in the knockout mice (45). the catalytic domain and appears to function as Deletion of the β1 subunit is generally viewed

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as a global sGC knockout because α1andα2 the α-andβ-proteins. Each sGC subunit con- do not form functional heterodimers with β2. sists of four distinct domains. The β1 subunit sGC α1andα2 knockout mice have also been contains a N-terminal heme-binding domain, PAS: protein fold named for its generated. Both proteins were found to be a Per/Arnt/Sim (PAS) domain, a coiled-coil association with the essential for long-term potentiation (46), and domain, and a C-terminal catalytic domain Per, ARNT, and Sim vasodilation was mediated primarily by the α1 (Figure 2) (reviewed in Reference 59). proteins isoform (47). In addition to clarifying the role of H-NOX: heme-nitric the α1β1 protein in NO-mediated pulmonary oxide and oxygen vasodilation (48, 49), studies with α1 subunit- Heme-Nitric Oxide and Oxygen binding deﬁcient mice suggest that both α-subunits are Binding Domain involved in gastric nitrergic relaxation (50) and Experiments with sGC truncations and site- relaxation of colon tissue (51). directed mutants were necessary to localize the Several invertebrates also contain genes minimal heme-binding domain of sGC. These that encode predicted NO-sensitive guanylate experiments involved the systematic mutation cyclases. Likely owing to the genetic tools of conserved histidines (60), expression of var- available in D. melanogaster, this organism ious truncations in E. coli (29), and deletion contains the best-characterized insect guany- of the β1 N terminus (61). Taken together, late cyclase. In D. melanogaster,Gycα-99B these studies showed that the β1 N terminus and Gycβ-100B are orthologs of the α1and constituted the heme-binding domain and sug- β1 subunits, respectively. Drosophila mutants gested that histidine 105 (rat) was the proximal deﬁcient in the production of these proteins heme ligand. The sGC heme-binding domain suggest that the NO/cGMP pathway mediates has been localized to residues 1 to ∼194 on a behavioral phenotype (52) and development the β1 subunit (28). Like the full-length sGC, of the visual system (53), and this pathway is the isolated heme domain binds NO and CO,

important for larval foraging locomotion (54). but not O2. The N terminus of the α1 subunit In other organisms, several biochemical studies has homology to the β1 N terminus and was have been aimed at elucidating the signiﬁcance shown to have afﬁnity for heme despite lacking of the NO/cGMP-signaling pathway. As men- the proximal histidine ligand (30). The sGC N tioned above, the full-length M. sexta α1β1 terminus is part of a conserved family of pro- heterodimer has recently been characterized teins found in both prokaryotes and eukaryotes (33). There is evidence that sGC in M. sexta is (62). This family of proteins has been termed involved in neuronal excitability (55) and odor heme-nitric oxide binding (62), sensor of nitric responsiveness (56). In mollusks, such as the oxide (63), and heme-nitric oxide and oxygen Limax marginatus and Limax maximus slugs, binding (H-NOX) (64). H-NOX is the most sGC may modulate the electrical oscillation of used abbreviation and will be used through-

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org interneurons in the central olfactory pathway out this review. To date, all of the character- (57, 58). ized H-NOX proteins bind heme as well as the

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. gaseous heme ligands NO and CO (reviewed in Reference 65). Some H-NOX proteins, includ- ARCHITECTURE OF SOLUBLE ing β1andβ2, discriminate against O2 bind- GUANYLATE CYCLASE ing, whereas others form a stable complex with

The rat sGC α1andβ1 subunits are 690 O2. In eukaryotes, H-NOX proteins have only and 619 amino acids in length, respectively. been found with the known sGC domain ar- These proteins are part of a large family of sGC chitecture. In bacteria, H-NOX domains can subunits that are conserved in eukaryotes. Gen- be found as proteins of ∼200 amino acids in erally, there is the highest sequence variability length with a single predicted function or as a at the N terminus of α-subunits and the great- domain within a larger protein on the basis of est sequence identity at the C terminus of both sequence analysis programs. Additionally, the

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genes that encode these H-NOX proteins in the α1 subunit (D485 and D529, rat number- bacteria are in proximity to genes that encode ing), which are predicted to bind two Mg2+ putative histidine kinases and diguanylate cy- ions (72). These residues are critical to catal- clases, or in some cases, a gene encodes the ysis as the associated metals likely activate both H-NOX as a domain within a larger protein, the nucleotide 3-hydroxyl and the α-phosphate often fused to a methyl-accepting chemotaxis for the reaction, as well as stabilize the charge domain. It is likely that these proteins have an on the β-andγ-phosphates on both the sub- evolutionarily conserved function and serve as strate and product. Additionally, β1 N548 is gas sensors in prokaryotes and eukaryotes. proposed to orient the ribose ring for the reaction. Residues thought to be responsible for base recognition include E473 and C541 on the Per/Arnt/Sim and Coiled-Coil β1 subunit. Other residues on both α1 (R573) Domains and β1 (R552) are thought to interact with the The central region of sGC contains two nucleotide triphosphate (72). With the identi- domains of unresolved function. The domain fication of these critical residues, predictions closer to the N terminus is predicted to adopt a can be made about guanylate cyclase activity PAS-like fold. Typically, PAS domains mediate using sequence analysis. This type of analysis protein-protein interactions and have often would correctly predict that the β2isoform been found to bind heme, a flavin, or a nu- could function as a homodimer but that β1, α1, cleotide (66). The other domain, a coiled-coil and α2 need a partner to be active. domain, appears to be unique to sGC and shares The catalytic domains have now been local- no significant homology with any other protein ized to the C-terminal 467–690 and 414–619 in the National Center for Biotechnology In- residues of the α1andβ1 subunits, respectively formation protein database (http://www.ncbi. (32). These catalytic domains must form a nlm.nih.gov/protein). The coiled-coil do- heterodimer for cGMP to be synthesized, and main of the rat β1 subunit (residues 348–409) in the full-length protein, the catalytic effi- was isolated as a tetramer and structurally ciency of the protein is dependent on the heme elucidated with X-ray crystallography (31). ligation state of the β1 H-NOX domain. sGC This structural study, in addition to experi- is highly selective for GTP as a substrate, but ments involving site-directed mutagenesis of the protein can also cyclize 2-d-GTP, GTP- residues on the α1 subunit (67), a bimolecular γ-S, guanosine 5-[β,γ-imido]-triphosphate fluorescence complementation assay in cells (GMP-PNP), ITP, UTP, and ATP (73–75).

(68), and structural analysis of homologs of the The isolated α1catβ1cat heterodimer is also sGC PAS domain (69), suggests that the central selective for GTP but can synthesize cAMP regions of both sGC subunits are important from ATP (76). Interestingly, the activity of

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org for the formation of a functional heterodimer. α1catβ1cat is inhibited by the presence of the H-NOX domain [β1(1–194) or β1(1–385)] 1,2 Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. (32). This shows that these domains interact Catalytic Domain in trans and suggests that the NO mechanism The C-terminal regions of the α1andβ1pro- of activation involves the relief of an inhibitory teins are highly homologous to the particulate interaction between the H-NOX domain guanylate cyclase and adenylate cyclase catalytic and the catalytic domains. In support of this domains. In the 1990s, structural insights on the sGC catalytic domains came from homol-

ogy models on the basis of crystal structures of 1 α1cat and β1cat are the catalytic domains of the rat sGC α1 the adenylate cyclase catalytic domains (70, 71). and sGC β1 subunits, respectively. These models identiﬁed key catalytic residues, 2β1(1–194) represents residues 1–194 of the rat sGC β1 including two conserved aspartate residues on subunit, the minimum heme-binding domain.

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proposal, a fluorescence (or Forster)¨ resonance genes code for subunits with greater homology energy transfer-based study showed that the to the β2 protein (Gyc-88E, Gyc-89Da, N terminus of both the α1andα2 subunits and Gyc-89Db) (81). Like β2, Gyc-88E can sGC homologs: proteins with high interact with the C terminus of the β1 subunit function as a homodimer, whereas Gyc-89Da sequence homology to (77). In addition to the heterodimeric rat sGC and Gyc-89Db are only active as heterodimers mammalian sGCs catalytic domains, the catalytic domain from (81). Experiments with cells overexpressing Atypical sGCs: the Chlamydomonas reinhardtii sGC (CYG12) Gyc-88E, Gyc-89Da, and Gyc-89Db indicate distinct subset of sGCs has been biochemically characterized (78). that cGMP synthesis in these cyclases is acti- with reduced This protein, as well as Synechocystis PCC6803 vated in the absence of O2 (80), and work with sensitivity to NO Cya2, a particulate guanylate cyclase (79), is purified protein confirms that the Gyc-88E

discussed in more detail below. homodimer forms a stable complex with O2 (82). As expected, Gyc-88E also binds NO SOLUBLE GUANYLATE and CO, but there are data that support the CYCLASE HOMOLOGS role of these proteins in mediating behavioral responses in hyperoxic environments in After the initial identification in mammals, it D. melanogaster (83). Interestingly, Gyc-88E was not until the emergence of genome se- is inhibited two- to threefold by the binding quencing that the prevalence of sGC and sGC ofNO,CO,andO, a property that is quite homologs in other organisms was fully realized. 2 distinct from the ligand-induced activation of Full-length guanylate cyclases with domain ar- the sGC α1β1 heterodimer. chitecture similar to the α1andβ1 subunits On the basis of sequence analysis, atypi- were found in several eukaryotic organisms. In cal sGCs exist in several organisms, includ- prokaryotes, sGC-like H-NOX domains were ing Caenorhabditis elegans (GCY-31-GCY-37); found as stand-alone proteins or fused to other however, worms do not contain a predicted functional domains (62). In some genomes, an NOS or NO-sensitive sGC. Seven β-like sGC-like PAS domain was also identified. To guanylate cyclases are contained within the date, the genes for sGC-like PAS domains are C. elegans genome, and it is likely that each gene always found near genes that encode sGC-like has an important functional role. GCY-35 is in- H-NOX domains (62). volved in social feeding (84), and both GCY-35 and GCY-36 promote aggregation and border- Eukaryotic Atypical Soluble ing behaviors (85). Significantly, these cGMP- Guanylate Cyclases dependent behavioral responses are mediated

As mentioned above, an increasing number by O2, which suggests the proteins function as of eukaryotic organisms are known to contain O2 sensors in vivo (84, 86). In support of this predicted sGCs. Some sGCs are very similar proposal, the GCY-35 H-NOX domain was

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org to the well-characterized rat α1andβ1 sub- isolated and shown to bind O2 (84). Analysis of units, whereas others vary signiﬁcantly. Collec- gcy-31 and gcy-33 mutants also implicates these

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. tively, these cyclases have been termed atypical genes in O2-dependent behavioral responses in sGCs (80), owing to their distinct activation and C. elegans, and the proteins encoded by these dimerization properties. Some atypical sGCs genes (GCY-31 and GCY-33) likely function exhibit a very surprising property—the ability in distinct sensory neurons (BAG versus URX)

to respond to O2. when compared to GCY-35 and GCY-36 (87). The D. melanogaster genome contains ﬁve Thus, a distinct class of cyclases exist, which

genes that code for sGCs. Two of these genes bind O2 and are inhibited by ligand binding, but code for subunits with high homology to the α1 there is currently no means to predict if a cy- and β1 proteins and have been shown to form clase is activated or inhibited by gaseous ligand a highly NO-sensitive heterodimeric sGC binding on the basis of sequence analysis. How- (Gycα-99B and Gycβ-100B). The other three ever, residues that contribute to gaseous ligand

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selectivity have been identiﬁed, as described below. NITRIC OXIDE SIGNALING IN BACTERIA

Prokaryotic Heme-Nitric Oxide A currently expanding topic within biological studies on NO in- and Oxygen Binding Proteins volves the role of the diatomic gas in bacterial signaling. NOS-like Several species of bacteria are known to contain proteins have been identiﬁed in several prokaryotic organisms, H-NOX proteins, and this number continues including Bacillus anthracis, Bacillus subtilis, Sorangium cellulosum, to increase as more genomes are sequenced. In- and Streptomyces turgidiscabies. Additionally, a wide range of bac- terestingly, all of the isolated H-NOX domains teria also have nitrite reductases, which generate NO as part of from facultative aerobes have ligand-binding denitrifying, assimilatory, and dissimilatory pathways. This en- properties like sGC, namely they do not dogenously produced NO is known to regulate several transcrip- bind O2. In facultative aerobes, the bacterial tion factors via S-nitrosation. There are also two potential classes members of the H-NOX family encode a single of prokaryotic heme-based NO sensors: globin-like proteins and

domain as a predicted stand-alone protein, H-NOX proteins. Microbial globin-like proteins bind O2,NO, and genes that encode either putative histidine and CO, and are thought to be involved in the nitrosative stress

kinases or diguanylate cyclases are found in response. Some H-NOX proteins bind O2, in addition to CO

the same predicted operon, suggesting that the and NO, whereas others exclude O2 binding. The genes that domain has a role in two-component signaling code for these H-NOX proteins are found in the same operons in bacteria. In support of this hypothesis, an as predicted histidine kinases or diguanylate cyclases. In vitro H-NOX domain and a predicted histidine studies have shown that the H-NOX protein and histidine kinase kinase from Shewanella oneidensis were isolated from S. oneidensis interact in a NO-dependent manner, but the and found to interact in vitro. Additionally, the physiological significance of this interaction is unknown. How- functional interaction between the H-NOX ever, NO is known to be important for the symbiosis between the and kinase was mediated by NO (88). Vibrio fis- bobtail squid and V. fischeri, where the H-NOX from V. fischeri cheri also contains an H-NOX protein, termed regulates colonization of the bacteria within the symbiotic host H-NOXVf , which is proposed to regulate a pu- squid by a mechanism that is dependent on NO. Further experi- tative histidine kinase. In V. fischeri,H-NOXVf ments in different microbial systems will likely uncover additional was shown to regulate genes involved in iron NO-dependent signaling processes in bacteria. uptake, and these same genes are modulated by the presence of NO (89), suggesting that = H-NOXVf mediates gene expression by sensing very stable heme-O2 complex (Kd 90 nM) NO. V. fischeri colonizes the light-emitting (90), a molecular distinction from the H-NOX organ of the Hawaiian bobtail squid, Euprymna domains from aerobic bacteria. The isolation scolopes, and it is likely that this mutualistic and characterization of the T. tengcongensis host-microbe symbiosis is mediated by a H-NOX domain have significantly influenced

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org NO/H-NOXVf interaction. Some bacteria, current understanding of sGC because it was like Rhodobacter sphaeroides and Nostoc puncti- the ﬁrst H-NOX domain to be structurally

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. forme, also encode a predicted PAS-like domain determined, and, moreover, it was crystallized upstream of the H-NOX gene (62). The func- bound to the diatomic ligand O2 (63, 64). tional signiﬁcance of this PAS domain to Thus far, these proteins have been used as bacterial signaling is unknown, but it has been tools for probing sGC structure and regula- proposed to mediate protein dimerization (69). tion, but functional studies in microbial systems In obligate anaerobes, such as Thermo- (see the sidebar titled Nitric Oxide Signaling nanaerobacter tengcongensis, the N-terminal in Bacteria) will be particularly interesting as H-NOX domain is fused to a C-terminal the variable ligand-binding properties of these methyl-accepting chemotaxis protein, suggest- H-NOXs may have consequences for their abil- ing a role in a chemotactic/signaling function. ity to respond to different gases, i.e., some pro- This H-NOX domain was found to form a teins may sense O2 in addition to NO or CO.

www.annualreviews.org • Structure and Regulation of SGC 541 BI81CH22-Marletta ARI 3 May 2012 12:17

H-NOX domain PAS domain CC domain Catalytic domain

Figure 3 Structures of heme nitric oxide and oxygen binding (H-NOX), PAS, coiled-coil (CC), and catalytic domains. The structures shown are the T. tengcongensis H-NOX domain [Protein Data Bank (pdb) code 1U55], the dimerized PAS domain from N. punctiforme PCC 73102 (pdb 2p04), the CC domain from the rat β1 subunit (pdb 3hls), and the homodimeric guanylate cyclase domain from C. reinhardtii (pdb 3et6).

STRUCTURAL INSIGHTS proteins. The proximal histidine, arginine, FROM STUDIES ON SOLUBLE and tyrosine had been previously identified as GUANYLATE CYCLASE AND critical residues for heme binding in the sGC β1 ITS HOMOLOGS subunit on the basis of mutagenesis studies (91, An increasing number of sGC homologs have 92), and the role of these residues became clear been isolated and characterized. Significantly, when the T. tengcongensis H-NOX structure was some of these homologs have been amenable solved. to crystallography, thus providing a foundation Another striking characteristic of the for structural proposals on the β1H-NOX, T. tengcongensis H-NOX structure is a highly PAS, and catalytic domains. The first crystal nonplanar heme conformation; it contains one structure of an sGC-like domain was that of of the most highly distorted hemes reported in

the O2-binding H-NOX domain (residues the Protein Data Bank. Interestingly, different 1–188) from T. tengcongensis (Figure 3) (63, molecules of the O2-bound H-NOX structure 64). This protein crystallized in two different exhibit varying degrees of deformation, sug-

six-coordinate heme states, with O2 bound gesting that the heme can exist in a range of con- to the reduced heme iron and in the oxi- formations. This proposal is supported by the dized heme state. These reports identiﬁed observation that the crystal structure of the H-

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org several amino acids with critical structural NOX protein from Nostoc sp. contains a moder- roles that are highly conserved within the ately distorted heme (93). This heme distortion

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. H-NOX family. Among the highly conserved is not an artifact of crystallization as it is also amino acids was the T. tengcongensis H-NOX observed in solution on the basis of an NMR heme-coordinating histidine (H102) and study of the S. oneidensis H-NOX (94) and reso- three residues that stabilize heme binding nance Raman experiments with T. tengcongensis (Figure 4). Speciﬁcally, arginine (R135) is crit- H-NOX (95) and α1β1 sGC (96–98). In fact, ical to the coordination of the heme propionate the dynamic range of heme conformations can groups and forms a hydrogen bond with both be accessed in solution by site-directed muta- YC-1: carboxyl groups, and tyrosine (Y135) and serine genesis (95) or, in the case of sGC, by addition 3-(5-hydroxymethyl- (S133) coordinate to one of the heme carboxyl of the allosteric activators YC-1 or BAY 41- 2 -furyl)-1-benzyl indazole groups. Together, these residues form a YxSxR 2272 (96–98). Speciﬁcally, the α1β1 sGC heme motif that is strictly conserved in H-NOX becomes more planar upon activator binding;

542 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

αA

αD N74

α G Y140 W9

αF H102

Figure 4 Distal heme pocket of the T. tengcongensis H-NOX domain [Protein Data Bank (pdb) 1U55 code]. Residues important to ligand selectivity (W9, N74, and Y140) and heme binding (H102) are shown. Image reproduced with permission of Elsevier (65).

however, it is unclear if this is a cause or con- speculation on a molecular mechanism of sGC sequence of enzyme activation. Thus, although activation. Specifically, the differential pivoting the functional importance of heme distortion and bending in the H-NOX heme upon NO or in sGC activation remains unknown, there is CO binding was suggested to account for the a potential to utilize changes in distortion in varying degree of activation induced by the two biological responses. ligands (200-fold versus fourfold, respectively) Among the residues thought to be critical to (93). In support of this proposal, an UV maintaining the nonplanar heme conformation resonance Raman study found that significant are I5, D45, R135 (in the YxSxR motif ), L144, conformational changes occurred at the N and P115, all of which are highly conserved terminus of sGC upon activator binding (96). in H-NOX proteins (64). In T. tengcongensis In sGC, the breaking of the proximal iron H-NOX, mutation of proline 115 to alanine (Fe)-His bond is an essential event in the leads to relaxation of the distorted heme (95, activation by NO, and thus, a structure of a 99). This heme relaxation was not observed af- five-coordinate H-NOX protein would be very ter mutation of proline 118 to alanine (P115 in important. Although a five-coordinate NO T. tengcongensis H-NOX) in α1β1 sGC (96); complex has not yet been determined, there are

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org however, it is not surprising that additional two recently solved structures where the net residues or domain interactions are important effect is the severing of the proximal Fe-His

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. for maintaining the heme conformation in the bond; the solution structure of a S. oneidensis H- mammalian protein. NOX mutant (94) and the crystal structure of

The crystal structure of the non-O2-binding BAY 58-2667-bound Nostoc sp. H-NOX (101). H-NOX from Nostoc sp. has been solved in Wild-type S. oneidensis H-NOX was shown to the ﬁve-coordinate unligated state and as the modulate the activity of a histidine kinase in six-coordinate NO- and CO-heme complexes a ligand-dependent manner: Kinase activity (93). Nostoc sp. H-NOX could function as a is inhibited by the FeII-NO H-NOX but not redox or NO sensor (100). Comparison of the the FeII-unligated H-NOX (88). The H103G T. tengcongensis H-NOX and Nostoc sp. H-NOX FeII-CO mutant mimics the kinase-inhibitory structures in different ligation states (FeII-CO, activity of the wild-type FeII-NO H-NOX (94). FeII-NO, and FeII-unligated states) led to Because H103 is the proximal iron ligand in

www.annualreviews.org • Structure and Regulation of SGC 543 BI81CH22-Marletta ARI 3 May 2012 12:17

S. oneidensis H-NOX, mutation of this residue This structure indicates that the coiled-coil do- to glycine leads to the isolation of apoprotein. main forms a tetramer composed of a dimer Similar to previous reports with other heme of dimers. In addition to identifying potential proteins (92, 102), heme binding in S. oneidensis residues involved in mediating dimerization, H-NOX H103G can be rescued by imidazole. the authors propose that interhelix salt-bridge H103 is in α-helix F, and in the heme-binding formation selects for heterodimerization versus rescued mutant, this helix is free to adopt a homodimerization in sGCs on the basis of their position like that in a five-coordinate NO structure (31). complex. The S. oneidensis H103G H-NOX The catalytic domains of two different func- structure, along with the structure of the tional guanylate cyclases (78, 79), and the in- weakly active wild-type FeII-CO S. oneidensis active human β1β1 catalytic domains [Protein H-NOX, was solved by NMR. The solution Data Bank (pdb) code 2WZ1], have been struc- structures of both of these proteins indicate turally elucidated (Figure 3). The functional that major changes in heme planarity and cyclase domains include a soluble homodimeric H-NOX conformation occur upon cleavage of guanylate cyclase from the eukaryotic algae the proximal histidine heme ligand. C. reinhardtii (78) and a particulate homo- Major structural changes are also observed dimeric guanylate cyclase from the unicellular between the unbound and BAY 58-2667- cyanobacterium Synechocystis PCC6803 Cya2 bound Nostoc sp. H-NOX structures (101). (79). Both proteins cyclize GTP and likely BAY 58-2667 is a NO- and heme-independent contain two catalytic sites per dimer. On the sGC activator (103) and is a candidate to treat basis of kinetic analysis of cGMP synthesis, the decompensated heart failure. The crystal struc- eukaryotic algae catalytic domains exhibit pos- ture shows that BAY 58-2667 is able to displace itive cooperativity with a Hill coefficient of 1.5. the heme and occupy the heme-binding site, This is similar to the cooperativity observed thereby leading to a shift in the α-helix F that in particulate guanylate cyclases and may be a contains the proximal histidine residue. Addi- common feature of homodimeric sGCs (78). tional experiments mutating residues around The α1β1 heterodimer contains one active site the proximal histidine on α-helix F suggest that and a proposed pseudosymmetric site. This D102 could play a critical role in enzyme activa- proposed pseudosymmetric site is thought tion (104). In addition to providing a structural to constitute an allosteric nucleotide-binding basis for proposals on sGC activation, these site that communicates with the catalytic H-NOX structures enabled the development nucleotide-binding site. On the basis of the of homology models of the heme-binding algae sGC structure, this communication may domains of both NO-sensitive and atypical cy- involve residues contained on the β2-β3 loop clases (28, 63, 105, 106), as well as density func- of each catalytic domain monomer. Specifically,

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org tional theory analysis and computer simulations the interaction of D527 or E523 (C. reinhardtii to address questions concerning structural sGC numbering) with a nucleotide in one

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. dynamics (107, 108). active site could alter the loop conformation The crystal structure of a domain from the and thus lead to a conformational change in N. punctiforme signal transduction histidine ki- the other nucleotide-binding site (78). nase has also been determined (Figure 3). This Unfortunately, both structures are in an domain has high sequence identity (35%–38%) inactive state, but they conﬁrm the guanylate to the sGC PAS domain, and the crystal struc- cyclase residues critical to metal binding and ture showed that the domain dimerized and nucleotide recognition that were predicted adopted a PAS fold (69). There is no struc- from the adenylate cyclase crystal structures. ture of a eukaryotic sGC PAS domain, but the Together, the reports of the C. reinhardtii crystal structure of the coiled-coil domain of sGC and Cya2 catalytic domains provided the the β1 subunit has been solved (Figure 3) (31). ﬁrst structures of a guanylate cyclase, and the

544 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

structures show that there is high homology the absence of a hydrogen bond donor in the between guanylate cyclase and adenylate α1β1 distal heme pocket, and the subsequent

cyclase domains; however, the elucidation of increase in the O2 off rate, likely contributes a mammalian heterodimeric structure remains to the protein’s inability to form a stable FeII-

an important task for understanding sGC O2 complex (64, 90). Molecular dynamics simu- regulation. Details about how movement in lations of O2-binding and non-O2-binding H- the β1 H-NOX domain affects the catalytic NOX proteins suggest that they have varying domain, and the role of the PAS and coiled-coil tunnel systems, which may also contribute to domain in relaying a signal from the H-NOX their different ligand-binding properties (112), domain, may remain open questions until the and site-directed mutagenesis within the pro- full-length sGC structure is elucidated. posed tunnel indicates that it is important for diffusion of gaseous ligands (113). Several biochemical studies aimed at LIGAND SELECTIVITY probing ligand selectivity in sGC have been The α1β1 heme environment is unique when reported. The distal-pocket tyrosine in the

compared to the globins because the cofactor O2-binding T. tengcongensis H-NOX was efﬁciently binds NO while having no afﬁnity mutated to leucine (Y140L), and this mutation

for O2. Additionally, the α1β1 heterodimer ex- signiﬁcantly reduced O2 afﬁnity. Additionally, hibits an extremely slow rate of oxidation and the introduction of a distal-pocket tyrosine in a

has among the highest midpoint potential re- non-O2-binding H-NOX from Legionella pneu- ported for a high-spin heme protein (+187 mV mophilia (L2 H-NOX) enabled the protein to

versus +58 mV for myoglobin) (109). This abil- bind O2 (90). Mutagenesis studies introducing ity of mammalian sGC to select against O2 a tyrosine into the distal pocket of the β1H- binding is important for it to function as a NO NOX-PAS domain β1(1–385) also produced a

sensor, as O2 is present at much higher levels protein that was capable of binding O2 (90), but II than NO in vivo, and Fe -O2 proteins react the same mutation in full-length sGC did not III rapidly with NO. Hemoproteins in the Fe facilitate O2 binding (106, 114). However, the oxidation state also form weak NO complexes introduction of a tyrosine and glutamine into and could inadvertently serve as a sink for NO. the β1 heme pocket (I145Y/I149Q) resulted in Since the discovery of sGC, several potential a full-length α1β1 protein with altered reactiv-

mechanisms of ligand discrimination against ity to O2 (105). A homology model of the O2- O2 have been proposed, including a weak Fe- binding guanylate cyclase Gyc-88E places these His bond strength, a negatively charged distal amino acids within the predicted distal heme

pocket, and a sterically constrained distal pocket pocket. Thus, some O2-binding guanylate cy- (109–111). One proposal on the mechanism by clases may utilize a Tyr/Gln hydrogen-bonding

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org which α1β1 excludes O2 is based on analysis of network, similar to several truncated globins the T. tengcongensis H-NOX crystal structure (115–118), to stabilize ligand binding. The

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. (63, 64). T. tengcongensis H-NOX stabilizes O2 marked variability in O2 reactivity between full- binding with a hydrogen-bonding network in- length sGC and heme-binding truncations of volving a tyrosine (Y140), a tryptophan (W9), the β1 protein highlights the potential for other and an asparagine (N74) (Figure 4). These sGC domains to inﬂuence ligand selectivity. residues appear to be absent in the β1H-NOX Thus, despite signiﬁcant progress in our under-

protein and other O2-excluding H-NOXs on standing of ligand discrimination in sGC, in- the basis of primary sequence alignments and cluding the identiﬁcation of residues critical for

homology modeling. Conversely, several atyp- stabilizing O2 binding in sGC homologs, there ical sGCs, including the known O2-binding cy- remain some unknown variables that may con- clase Gyc-88E, encode a tyrosine that aligns tribute to the ligand speciﬁcity of these heme with T. tengcongensis H-NOX Y140. Therefore, proteins.

www.annualreviews.org • Structure and Regulation of SGC 545 BI81CH22-Marletta ARI 3 May 2012 12:17

REGULATION OF SOLUBLE five-coordinate sGC-NO complex, and GUANYLATE CYCLASE BY this effect is blocked by the addition of ATP NITRIC OXIDE (122, 123). Breakage of the Fe-His bond is thought to Physiological responses to NO, such as smooth be a critical step in the activation of sGC by muscle relaxation, are rapidly induced by low NO; however, recent data have shown that NO levels of the diatomic gas. In cells, cGMP coordination to the heme is not sufficient for levels rise within milliseconds after exposure full activation ex vivo (122, 123). A low-activity to nanomolar concentrations of NO, and this FeII-NO complex can be formed in the pres- fast response occurs because sGC efficiently ence of stoichiometric amounts of NO, whereas binds to and is activated by NO. When NO a high-activity FeII-NO complex is formed in dissociates from the protein, the amount of the presence of excess NO. These two five- cGMP decreases to a basal level. Thus, both coordinate FeII-NO species are indistinguish- the rise and fall of cGMP levels must be tightly able by electronic absorption spectroscopy, but regulated for proper function of cGMP- they exhibit distinct signals by electron para- dependent processes. Upon repeated exposure magnetic spectroscopy (124). Preincubation of to NO or NO-donors, like GTN, maximal sGC with substrate Mg2+GTP or the reaction sGC activation decreases, and this process is products Mg2+/cGMP/PP produces a high- called sGC desensitization. sGC activation, i activity FeII-NO species in the presence of deactivation, and desensitization have been stoichiometric amounts of NO (123). ATP can extensively studied in vivo and in vitro. A major compete with the GTP effect, and in the pres- challenge with understanding these processes ence of ATP and GTP, a low-activity FeII-NO occurs when reconciling discrepancies in species is formed (122). This clear difference results obtained with purified protein versus in sGC activity indicates that preincubation sGC examined in the cellular milieu. of the enzyme with the small molecules leads to a conformational change such that sGC is highly activated by low levels of NO. It was Activation and Nitric also found that the small-molecule YC-1 can Oxide Association activate the low-activity FeII-NO complex to As mentioned above, the activation of sGC the high-activity state (122, 125). Thus, both in vitro and in vivo is rapid (occurs in mil- YC-1 and excess NO activate the low-activity liseconds). Using a NO donor or NO gas, five-coordinate FeII-NO complex that is the apparent 50% effective concentration for formed in the absence of substrate or reaction NO acting on purified sGC is between 80 and products. 250 nM (119, 120). A similar potency of NO Two mechanisms have been proposed to ac- II Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org has been measured in rat cerebellar cells (ap- count for the varying activity of the sGC Fe - parent 50% effective concentration ∼45 nM) NO complex observed ex vivo. One proposal II Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. (121). On the basis of studies with purified is that excess NO activates the Fe -NO com- protein, it is known that NO binds to the heme plex by binding to nonheme sites on the pro- of sGC at a diffusion-controlled rate to form an tein (122). If NO binds to a nonheme site, initial six-coordinate complex, which rapidly it is likely that cysteines would comprise this converts to a five-coordinate ferrous nitrosyl binding site as experiments with the thiol reac- (FeII-NO) complex (120). The six-coordinate tive reagent methyl methanethiosulfonate sug- FeII-NO complex is not stable and has only gest that reduced cysteines are necessary for the been observed with time-resolved spectro- mechanism of NO activation (125). The second scopic methods (120, 122, 123). The presence proposal regarding sGC activation involves ex- of Mg2+GTP or Mg2+/cGMP/pyrophosphate cess NO binding to the heme to form a tran-

(PPi) accelerates the formation of the sient dinitrosyl complex, which then converts

546 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

In vitro measurements NO dissociation

NO NO Slow Slow Preincubation with GTP increases rate FeII FeII FeII ATP inhibits this GTP effect His His His 399 nm 399 nm 431 nm YC-1 or BAY 41-2272 increases rate

Deactivation

NO NO NO Fast No effect with GTP or ATP FeII FeII YC-1 decreases rate His His

High activity Low activity

Figure 5 Model of nitric oxide (NO) dissociation and deactivation of NO-stimulated soluble guanylate cyclase (sGC) in vitro. The sGC-NO complex consists of two different ﬁve-coordinate species that slowly interconvert. NO dissociation from the sGC heme is slow, whereas NO deactivation is rapid on the basis of in vitro measurements, including spectroscopic methods (Absmax indicated in nanometers) and cyclic GMP analysis. The presence of allosteric modulators (GTP, ATP, YC-1, or BAY 41-2272) inﬂuences the deactivation and NO dissociation rates differently. Taken together, these results indicate that the deactivated sGC species is distinct from the unligated sGC species (431 nm) produced from NO dissociation from the heme and suggests that two molecules of NO are able to bind to sGC.

to a five-coordinate complex with NO bound in lifetime of the NO signal in vivo. This process the proximal heme pocket (123). Such proximal was originally thought to correlate directly with heme pocket NO binding has been observed NO dissociation from the sGC heme; however, with other histidine-ligated heme proteins in- as mentioned above, a NO-bound protein that cluding cytochrome c (126). is partially activated has been characterized. The importance of the two different sGC- This indicates that sGC deactivation and NO NO states in vivo remains unclear. One report dissociation from the heme cofactor are not examining sGC activity in endothelial cells explicitly linked, and thus, deactivation and proposed that enzyme activation by excess NO heme-NO dissociation measurements cannot is important for the physiological activation of be used interchangeably (Figure 5). Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org sGC (125), whereas another report examining NO-induced relaxation of smooth muscle sGC activation in rat platelets and cerebellar cells dissipates within seconds upon removal of Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. cells proposed that the observed activation free NO due to the deactivation of sGC (128). kinetics were consistent with a single NO- sGC deactivation, the rate of decline in cGMP binding event (127). Thus, further experiments synthesis after an activator is removed, has are necessary to resolve the mechanism of sGC been determined in various cells and with puri- activation in vivo. fied protein. In cells, sGC deactivation is rapid ◦ (t1/2 < 5sat37 C)inthepresenceofanNOtrap Deactivation and Nitric (oxyhemoglobin) to limit NO rebinding (121, Oxide Dissociation 129). Activity assays with the cytosol of retina Deactivation of the sGC FeII-NO complex homogenate indicate that the sGC-NO deac- has been extensively studied to understand the tivation rate is not influenced by the presence

www.annualreviews.org • Structure and Regulation of SGC 547 BI81CH22-Marletta ARI 3 May 2012 12:17

of Mg2+GTP and is only slightly increased by Desensitization the presence of reducing agents, such as glu- The sGC response to GTN or NO decreases tathione and dithiothreitol (129). In agreement S-nitrosation: upon repeated exposure to the activators. This posttranslational with cellular data, the deactivation rate of pu- desensitization is rapid, such that a single ∼ ◦ modification involving rified protein is also rapid (t1/2 4sat37C) pretreatment of cells with GTN or NO can the oxidative addition (130). This deactivation rate is unaffected by the significantly reduce cGMP stimulation upon of NO to a thiol presence of a GTP analog and/or ATP (122), the second exposure (132, 133). Purified but the rate is significantly decreased (140-fold) protein in the absence of reducing agents also by the presence of the allosteric activator YC-1 exhibits a decrease in NO-stimulated activity > ◦ (t1/2 10 min at 37 C) (130). after pretreatment with NO. This desensiti- The rate of NO dissociation from the sGC zation has implications for therapies used in heme must be spectroscopically determined, the treatment of heart disease as this loss of and as a consequence, this rate has only been responsiveness, or tolerance, is also observed measured in vitro. Early reports found that when organic nitrates are administered to the sGC heme-NO complex is very stable patients with angina pectoris (134). As a conse- ∼ ◦ (t1/2 87 min at 37 C) in the absence of NO quence, these drugs cannot be used repeatedly. traps or allosteric effectors (23, 131). Unlike Over the past 30 years, several proposals have most heme proteins, which rapidly oxidize in been advanced to explain the phenomenon of II thepresenceofO2 and NO, a reduced Fe tolerance, including increased PDE activity protein is formed when NO dissociates from (135), inhibition of mitochondrial aldehyde the sGC heme. Using a trap to scavenge NO, dehydrogenase (136), and most recently like CO/dithionite or oxymyoglobin, the dis- S-nitrosation (137, 138). There is currently sociation rate can be determined without in- significant evidence in support of the proposal terference from NO rebinding. Reductants like that nitrosation, the oxidative addition of NO dithiothreitol or glutathione react with NO and to a thiol, contributes to sGC desensitization. can also be used to prevent rebinding (23). With It has long been known that thiol oxidation these NO trapping methods, it was determined inhibits sGC activity. Cysteines can oxidize that the NO dissociation rate is relatively slow sequentially to form a sulfenic acid, sulfinic = ◦ (t1/2 3–8 min at 37 C) (23, 27, 131) com- acid, sulfonic acid, or a disulfide bond in the pared to previously determined deactivation presence of O2, or form a nitrosothiol in the rates but increases (∼50-fold) in the presence presence of NO and O2. In the 1980s, the for- 2+ 2+ of Mg GTP (131). However, if Mg GTP is mation of sGC-cysteine mixed disulfides was added to sGC after the NO complex is formed, shown to reversibly inhibit cGMP production it has no effect on the dissociation rate (23, 123, (139). More recently, the induction of reactive 131), indicating that the allosteric affect of GTP O2 species in vascular smooth muscle cells was Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org is dependent on substrate binding in the ab- found to inhibit cGMP synthesis and lead to the sence of NO. In contrast to the previously dis- oxidative modification of sGC cysteines (140). Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. cussed deactivation results, the GTP effect on Additionally, the thiol modifying reagent the dissociation rate is inhibited by the pres- methyl methanethiosulfonate was shown to ence of ATP (122). Therefore, in the presence inhibit sGC activity in vitro and in primary of both GTP and ATP, sGC exhibits a slow endothelial cells. In vitro sGC inhibition by NO dissociation rate but rapid deactivation. In methyl methanethiosulfonate is reversible, and thepresenceofYC-1,theNOdissociationrate the molecule was shown to modify several increases (27), whereas the deactivation rate de- cysteines on both the α1andβ1 subunits creases (130). A model summarizing deactiva- (125). The NO-dependent oxidation of cys- tion of sGC and NO dissociation is shown in teines on sGC has also been reported. sGC Figure 5. is S-nitrosated in the presence of low levels

548 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

of NO, and this modification has been linked only weakly activate the protein (17, 141, 142). to a reduction in NO-stimulated activity The binding of these compounds leads to the (137). In addition, GTN has been shown to formation of a six-coordinate complex and to a Nitrate tolerance: induce sGC S-nitrosation and desensitization two- to fourfold increase in the rate of cGMP loss of sensitivity to in a concentration-dependent manner (138). production, significantly lower than the 100- to nitrates Cysteines on both the α1 (C243) and β1 400-fold increase in cGMP synthesis observed (C122) subunits have been identified as targets with NO. Other compounds that have been re- of this oxidative modification. ported to activate sGC by targeting the heme- It has become clear that sGC requires free binding pocket include protoporphyrin IX (15) thiols for proper function. Without a crystal and Co2+ protoporphyrin IX (143). structure, it is difficult to address why these cys- It has become clear that small molecules teines are necessary for NO-induced sGC acti- can modulate the activity of sGC and that vation. Perhaps free thiols are important to the new therapeutics might be developed for the structural integrity of the protein, involved in a treatment of various diseases. This prompted conformational change to the activated enzyme a search for novel sGC activators, and several state, and/or directly involved in the NO mech- compounds were screened for the ability to in- anism of activation. If sGC S-nitrosation is the crease cGMP levels in cell lysates. Such a screen primary molecular mechanism of nitrate toler- led to the identification of YC-1, a benzylin- ance, then molecules developed to protect these dazole derivative that activates sGC without thiols from oxidation could be useful for the coordinating to the heme (144). YC-1 only treatment of diseases related to sGC dysfunc- activates the FeII-unligated sGC state two- to tion. Furthermore, the apo- and heme-oxidized fourfold but significantly increases sGC activity sGC states have been proposed to be physiolog- when a ligand is bound at the FeII heme (141, ically relevant sGC species in diseased tissue. 142, 145, 146). This synergistic activation leads to an FeII-CO complex that is activated 100- to 400-fold and an FeII-NO complex that is MODULATORS OF SOLUBLE activated 200- to 800-fold. The molecular GUANYLATE CYCLASE ACTIVITY mechanism of YC-1 activation is unknown. Experiments with equilibrium dialysis suggest Soluble Guanylate Cyclase Activators that sGC binds one equivalent of YC-1 per sGC is a therapeutic target in the treatment heterodimer (147). This binding site may of heart disease. Organic nitrites and organic be contained within the N terminus of the nitrates (like GTN) are perhaps the earliest α1 subunit (33, 148) or within the pseu- agents used to target the NO/cGMP-signaling dosymmetric substrate site (149–151). What pathway and have been in clinical use for over is clear is that YC-1 binding to sGC induces

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org 100 years. The ﬁrst description of GTN as a a conformational change that elevates cGMP therapeutic agent for the treatment of angina production. This highly active conformational

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. pectoris appeared in 1879, and it remains the state has been characterized by spectroscopic drug of choice to treat the disease. Despite methods, including electronic absorption decades of clinical use, the precise mechanism (152), resonance Raman spectroscopy (147, of action of GTN is unknown; however, it 153), and electron paramagnetic resonance is generally considered a nitrovasodilator or spectroscopy (124, 147). There are also clear a NO-donor. This NO release may occur by kinetic effects of adding YC-1 to CO- or spontaneous decomposition or bioconversion NO-bound sGC (27, 130, 154). to result in NO-dependent sGC activation. The discovery of the novel sGC stimulator In addition to NO, other known heme lig- YC-1 led several groups to carry out structure ands, including CO, nitrosoalkanes, and alkyl activity relationships to improve both the sol- isocyanides, can bind to the sGC heme but can ubility and efﬁcacy of YC-1. With this work

www.annualreviews.org • Structure and Regulation of SGC 549 BI81CH22-Marletta ARI 3 May 2012 12:17

came the identification of several other com- Soluble Guanylate Cyclase Inhibitors pounds, including BAY 41-2272, BAY 41-8543, There has been significantly more work on CMF-1571, and A-350619 (reviewed in Refer- identifying sGC activators, but compounds ence 103). Although there is some debate over that inhibit sGC activity have also been re- the possible inhibition of PDE5 by BAY 41- ported. These compounds are not as selec- 2272 (155, 156), it is commonly accepted that tive as the identified activators and include the molecule activates sGC without coordinat- general oxidants, molecules that target hemo- ing to the heme. Collectively, these molecules proteins, and nucleotide cyclase inhibitors. constitute a novel class of sGC stimulators Compounds proposed to target the sGC H- that require the presence of the heme moiety NOX domain include heme, hematin (15), and have the ability to synergistically stimulate and 1H-[1,2,4]oxadiazolol[4,3-a]quinoxalin-1- sGC with both NO and CO. These molecules one (ODQ) (166). These compounds inhibit were promising drug candidates but had un- sGC by oxidation of the ferrous iron in favorable drug metabolism. Medicinal chem- the heme cofactor. Molecules such as hy- istry efforts to reduce the problems associated drogen peroxide, superoxide, cystine, and S- with these compounds led to the discovery of nitrosocysteine also reduce cGMP production BAY 63-2521 (riociguat). This compound in- by oxidizing critical residues on sGC (138– duces vasodilation by activating sGC and is cur- 140). Other known sGC inhibitors, such as rently in Phase III clinical trails (reviewed in LY83583 (167) and methylene blue (168), in- Reference 157). hibit the enzyme via generation of super- There are also small-molecule activators oxide anion (169, 170). Inhibition of sGC that target heme-oxidized or -deficient sGC; by these oxidants emphasizes the importance therefore, they are classified as NO and heme of the redox environment for proper protein independent. One of these is BAY 58-2667 function. (Cinaciguat) (158). BAY 58-2667 is generally Substrate analogs that bind to the sGC cited as an activator of both heme-deficient catalytic domain inhibit guanylate cyclase and heme-oxidized (FeIII) sGC (158), but there activity. To date, several such analogs have is one report that proposes the molecule ex- been identified as sGC inhibitors, including, clusively targets the heme-deficient sGC state but not limited to, ITP, XTP, CTP, ATP, (159). BAY 58-2667 is proposed to activate sGC ADP, AMP, 2 -deoxyadenosine 5 -diphosphate by binding within the heme pocket, thereby (2 -dADP), GDP, guanosine-5 -[(α,β)- serving as a mimic of the heme-NO complex methylene]triphosphate (GMP-CPP), and (91, 101). In addition to activating the en- N-methylanthraniloyl (MANT)-nucleotides zyme, BAY 58-2667 also stabilizes sGC and (75, 151, 171, 172). These compounds inhibit protects the protein from degradation (160). In sGC by varying mechanisms depending on

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org rats, BAY 58-2667 was shown to lower blood whether they target the pseudosymmetric site pressure (161) and protect against ischemic in- in addition to the substrate-binding site. For

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. jury (162), and the compound has been tested example, AMP-PNP is a competitive inhibitor on patients with acute decompensated heart (151), while ATP is a mixed-type inhibitor and failure (163–165). substrate (76).

SUMMARY POINTS 1. Soluble guanylate cyclase (sGC) is the most thoroughly characterized receptor for the signaling molecule nitric oxide (NO). NO activation of sGC is essential to several physiological processes, and thus dysfunction in sGC is linked to several diseases. Compounds that modulate sGC are in clinical trails for the treatment of heart disease.

550 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

2. Each sGC subunit consists of an H-NOX, PAS, coiled-coil, and catalytic domain. Func- tional truncations of sGC include the isolated β1 H-NOX domain, the β1 coiled-coil domain, and the α1β1 catalytic domains. 3. Genome mining has revealed that several predicted proteins exist with high sequence homology to sGC, including prokaryotic H-NOXs and eukaryotic NO-sensitive and atypical sGCs. 4. The structure of full-length sGC is not yet determined, but studies on H-NOXs and sGC homologs have illuminated many important structural features of the enzyme. On the basis of these studies, sGC likely contains a hydrophobic heme-binding pocket, without a distal-pocket hydrogen bond donor, and heterodimerization is mediated by contacts on the PAS, coiled-coil, and catalytic domains.

5. α1β1 sGC does not form a stable complex with O2, but several sGC homologs bind O2. Hydrogen bond donors in the heme-distal pocket are often found in the H-NOXs and

atypical sGCs that bind O2. The presence or absence of amino acids capable of forming a hydrogen bond in the heme-distal pocket contributes to selectivity for gaseous ligands. 6. sGC regulation by NO and nucleotides in vitro is complex. Two molecules of NO can bind to the protein, and both GTP and ATP can inﬂuence NO binding, dissociation, and activation. In cells, it is likely that NO, GTP, and ATP modulate cGMP production, and both reduced cysteines and a reduced heme iron are important for this activity.

FUTURE ISSUES Over the past few years, sGC has been implicated in an expanding number of physiological processes and diseases. Continued progress toward elucidating the mechanism of sGC activation is important in the development of therapeutics to treat disorders relating to the NO-signaling pathway. Despite signiﬁcant advances in our understanding of NO as a signaling agent, many questions remain unanswered. In mammals, the sGC response to NO is complicated, and the precise events that lead to activation remain a topic of debate. Furthermore, sGC is regulated by allosteric interactions with ATP and GTP, and there are likely other important factors, including S-nitrosation and phosphorylation, that modulate sGC activity. Future experiments considering these factors will be necessary to determine the inﬂuence of each regulatory factor in the activation, deactivation, and desensitization of Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org sGC. How do the α1andβ1 subunits interact when sGC is activated? What is the nature of the allosteric activator-binding site? What conformational changes occur when ligands Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. bind to sGC? All of these questions may be addressed with the structural elucidation of the full-length heterodimeric protein. Additionally, structural analysis may provide insight into the molecular mechanisms that lead to sGC dysfunction.

DISCLOSURE STATEMENT M.A.M. is a cofounder of Omniox, Inc., a company commercializing oxygen delivery technology for a broad range of clinical indications in cancer, surgical, and cardiovascular markets. The authors are not aware of any other afﬁliations, memberships, funding, or ﬁnancial holdings that might be perceived as affecting the objectivity of this review.

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ACKNOWLEDGMENTS This article was written while M.A.M. was employed by the University of California, Berkeley. The authors acknowledge members of the Marletta lab, past and present, who have contributed to studies on sGC, NOS, and H-NOXs. Research on sGC in the authors’ laboratory was supported by the National Institutes of Health (NIH grant GM077365), and research on H-NOXs by NIH grant GM070671.

LITERATURE CITED 1. Brunton TL. 1867. On the use of nitrite of amyl in angina pectoris. Lancet 90:97–98 2. Murrell W. 1879. Nitro-glycerine as a remedy for angina pectoris. Lancet 113:113–15 3. Garbers DL, Chrisman TD, Wiegn P, Katafuchi T, Albanesi JP, et al. 2006. Membrane guanylyl cyclase receptors: an update. Trends Endocrinol. Metab. 17:251–58 4. Padayatti PS, Pattanaik P, Ma X, van den Akker F. 2004. Structural insights into the regulation and the activation mechanism of mammalian guanylyl cyclases. Pharmacol. Ther. 104:83–99 5. Feussner M, Richter H, Baum O, Gossrau R. 2001. Association of soluble guanylate cyclase with the sarcolemma of mammalian skeletal muscle fibers. Acta Histochem. 103:265–77 6. Russwurm M, Wittau N, Koesling D. 2001. Guanylyl cyclase/PSD-95 interaction: targeting of the nitric oxide-sensitive α2β1 guanylyl cyclase to synaptic membranes. J. Biol. Chem. 276:44647–52 7. Zabel U, Kleinschnitz C, Oh P, Nedvetsky P, Smolenski A, et al. 2002. Calcium-dependent membrane association sensitizes soluble guanylyl cyclase to nitric oxide. Nat. Cell Biol. 4:307–11 8. Madhani M, Okorie M, Hobbs AJ, MacAllister RJ. 2006. Reciprocal regulation of human soluble and particulate guanylate cyclases in vivo. Br.J.Pharmacol.149:797–801 9. Munzel T, Feil R, Mulsch A, Lohmann SM, Hofmann F, Walter U. 2003. Physiology and pathophysiol- ogy of vascular signaling controlled by guanosine 3,5-cyclic monophosphate-dependent protein kinase. Circulation 108:2172–83 10. Sanders KM, Ward SM, Thornbury KD, Dalziel HH, Westfall DP, Carl A. 1992. Nitric oxide as a non-adrenergic, non-cholinergic neurotransmitter in the gastrointestinal tract. Jap. J. Pharmacol. 58(Suppl.):P220–25 11. Warner TD, Mitchell JA, Sheng H, Murad F. 1994. Effects of cyclic GMP on smooth muscle relaxation. Adv. Pharmacol. 26:171–94 12. Garbers DL. 1979. Purification of soluble guanylate cyclase from rat lung. J. Biol. Chem. 254:240–43 13. Braughler JM, Mittal CK, Murad F. 1979. Purification of soluble guanylate cyclase from rat liver. Proc. Natl. Acad. Sci. USA 76:219–22 14. Gerzer R, Hofmann F, Schultz G. 1981. Purification of a soluble, sodium-nitroprusside-stimulated guanylate cyclase from bovine lung. Eur. J. Biochem. 116:479–86 15. Ignarro LJ, Wood KS, Wolin MS. 1982. Activation of purified soluble guanylate cyclase by protopor-

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org phyrin IX. Proc. Natl. Acad. Sci. USA 79:2870–73 16. Vogel KM, Hu S, Spiro TG, Dierks EA, Yu AE, Burstyn JN. 1999. Variable forms of soluble guanylyl

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. cyclase: protein-ligand interactions and the issue of activation by carbon monoxide. J. Biol. Inorg. Chem. 4:804–13 17. Stone JR, Marletta MA. 1994. Soluble guanylate cyclase from bovine lung: activation with nitric oxide and carbon monoxide and spectral characterization of the ferrous and ferric states. Biochemistry 33:5636–40 18. Russwurm M, Koesling D. 2005. Puriﬁcation and characterization of NO-sensitive guanylyl cyclase. Methods Enzymol. 396:492–501 19. Harteneck C, Koesling D, Soling A, Schultz G, Bohme E. 1990. Expression of soluble guanylyl cyclase. Catalytic activity requires two enzyme subunits. FEBS Lett. 272:221–23 20. Buechler WA, Nakane M, Murad F. 1991. Expression of soluble guanylate cyclase activity requires both enzyme subunits. Biochem. Biophys. Res. Commun. 174:351–57 21. Friebe A, Wedel B, Harteneck C, Foerster J, Schultz G, Koesling D. 1997. Functions of conserved cysteines of soluble guanylyl cyclase. Biochemistry 36:1194–98

552 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

22. Zhou Z, Gross S, Roussos C, Meurer S, Muller-Esterl W, Papapetropoulos A. 2004. Structural and functional characterization of the dimerization region of soluble guanylyl cyclase. J. Biol. Chem. 279:24935–43 23. Brandish PE, Buechler W, Marletta MA. 1998. Regeneration of the ferrous heme of soluble guanylate cyclase from the nitric oxide complex: acceleration by thiols and oxyhemoglobin. Biochemistry 37:16898– 907 24. Hoenicka M, Becker EM, Apeler H, Sirichoke T, Schroder H, et al. 1999. Puriﬁed soluble guanylyl cyclase expressed in a baculovirus/Sf9 system: stimulation by YC-1, nitric oxide, and carbon monoxide. J. Mol. Med. 77:14–23 25. Lee YC, Martin E, Murad F. 2000. Human recombinant soluble guanylyl cyclase: expression, puriﬁcation, and regulation. Proc. Natl. Acad. Sci. USA 97:10763–68 26. Wagner C, Russwurm M, Jager R, Friebe A, Koesling D. 2005. Dimerization of nitric oxide-sensitive guanylyl cyclase requires the α1Nterminus.J. Biol. Chem. 280:17687–93 27. Winger JA, Derbyshire ER, Marletta MA. 2007. Dissociation of nitric oxide from soluble guanylate cyclase and heme-nitric oxide/oxygen binding domain constructs. J. Biol. Chem. 282:897–907 28. Karow DS, Pan D, Davis JH, Behrends S, Mathies RA, Marletta MA. 2005. Characterization of functional heme domains from soluble guanylate cyclase. Biochemistry 44:16266–74 29. Zhao Y, Marletta MA. 1997. Localization of the heme binding region in soluble guanylate cyclase. Biochemistry 36:15959–64 30. Zhong F, Pan J, Liu X, Wang H, Ying T, et al. 2011. A novel insight into the heme and NO/CO binding mechanism of the alpha subunit of human soluble guanylate cyclase. J. Biol. Inorg. Chem. 16:1227–39 31. Ma X, Beuve A, van den Akker F. 2010. Crystal structure of the signaling helix coiled-coil domain of the β1 subunit of the soluble guanylyl cyclase. BMC Struct. Biol. 10:2 32. Winger JA, Marletta MA. 2005. Expression and characterization of the catalytic domains of soluble guanylate cyclase: interaction with the heme domain. Biochemistry 44:4083–90 33. Hu X, Murata LB, Weichsel A, Brailey JL, Roberts SA, et al. 2008. Allostery in recombinant soluble guanylyl cyclase from Manduca sexta. J. Biol. Chem. 283:20968–77 34. Harteneck C, Wedel B, Koesling D, Malkewitz J, Bohme E, Schultz G. 1991. Molecular cloning and expression of a new α-subunit of soluble guanylyl cyclase. Interchangeability of the α-subunits of the enzyme. FEBS Lett. 292:217–22 35. Yuen PS, Potter LR, Garbers DL. 1990. A new form of guanylyl cyclase is preferentially expressed in rat kidney. Biochemistry 29:10872–78 36. Budworth J, Meillerais S, Charles I, Powell K. 1999. Tissue distribution of the human soluble guanylate cyclases. Biochem. Biophys. Res. Commun. 263:696–701 37. Bellingham M, Evans TJ. 2007. The α2β1 isoform of guanylyl cyclase mediates plasma membrane localized nitric oxide signalling. Cell Signal. 19:2183–93 38. Russwurm M, Behrends S, Harteneck C, Koesling D. 1998. Functional properties of a naturally occurring isoform of soluble guanylyl cyclase. Biochem J. 335(Part 1):125–30 39. Behrends S, Harteneck C, Schultz G, Koesling D. 1995. A variant of the α2 subunit of soluble guanylyl cyclase contains an insert homologous to a region within adenylyl cyclases and functions as a dominant Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org negative protein. J. Biol. Chem. 270:21109–13 40. Neitz A, Mergia E, Eysel UT, Koesling D, Mittmann T. 2011. Presynaptic nitric oxide/cGMP facilitates

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. glutamate release via hyperpolarization-activated cyclic nucleotide-gated channels in the hippocampus. Eur. J. Neurosci. 33:1611–21 41. Koglin M, Vehse K, Budaeus L, Scholz H, Behrends S. 2001. Nitric oxide activates the β2 subunit of soluble guanylyl cyclase in the absence of a second subunit. J. Biol. Chem. 276:30737–43 42. Behrends S, Budaeus L, Kempfert J, Scholz H, Starbatty J, Vehse K. 2001. The β2 subunit of nitric oxide-sensitive guanylyl cyclase is developmentally regulated in rat kidney. Naunyn-Schmiedebergs Arch. Pharmacol. 364:573–76 43. Friebe A, Koesling D. 2009. The function of NO-sensitive guanylyl cyclase: What we can learn from genetic mouse models. Nitric Oxide 21:149–56 44. Friebe A, Mergia E, Dangel O, Lange A, Koesling D. 2007. Fatal gastrointestinal obstruction and hypertension in mice lacking nitric oxide-sensitive guanylyl cyclase. Proc. Natl. Acad. Sci. USA 104:7699– 704

www.annualreviews.org • Structure and Regulation of SGC 553 BI81CH22-Marletta ARI 3 May 2012 12:17

45. Groneberg D, Konig P, Wirth A, Offermanns S, Koesling D, Friebe A. 2010. Smooth muscle-specific deletion of nitric oxide-sensitive guanylyl cyclase is sufficient to induce hypertension in mice. Circulation 121:401–9 46. Haghikia A, Mergia E, Friebe A, Eysel UT, Koesling D, Mittmann T. 2007. Long-term potentiation in the visual cortex requires both nitric oxide receptor guanylyl cyclases. J. Neurosci. 27:818–23 47. Mergia E, Friebe A, Dangel O, Russwurm M, Koesling D. 2006. Spare guanylyl cyclase NO receptors ensure high NO sensitivity in the vascular system. J. Clin. Investig. 116:1731–37 48. Nimmegeers S, Sips P, Buys E, Brouckaert P, Van de Voorde J. 2007. Functional role of the soluble guanylyl cyclase α1 subunit in vascular smooth muscle relaxation. Cardiovasc. Res. 76:149–59 49. Vermeersch P, Buys E, Pokreisz P, Marsboom G, Ichinose F, et al. 2007. Soluble guanylate cyclase- α1 deficiency selectively inhibits the pulmonary vasodilator response to nitric oxide and increases the pulmonary vascular remodeling response to chronic hypoxia. Circulation 116:936–43 50. Vanneste G, Dhaese I, Sips P, Buys E, Brouckaert P, Lefebvre RA. 2007. Gastric motility in soluble guanylate cyclase α1 knock-out mice. J. Physiol. 584:907–20 51. Dhaese I, Vanneste G, Sips P, Buys E, Brouckaert P, Lefebvre RA. 2008. Involvement of soluble guanylate cyclase α1 and α2, and SKCa channels in NANC relaxation of mouse distal colon. Eur. J. Pharmacol. 589:251–59 52. Tinette S, Zhang L, Garnier A, Engler G, Tares S, Robichon A. 2007. Exploratory behaviour in NO- dependent cyclase mutants of Drosophila shows defects in coincident neuronal signalling. BMC Neurosci. 8:65 53. Gibbs SM, Becker A, Hardy RW, Truman JW. 2001. Soluble guanylate cyclase is required during development for visual system function in Drosophila. J. Neurosci. 21:7705–14 54. Riedl CA, Neal SJ, Robichon A, Westwood JT, Sokolowski MB. 2005. Drosophila soluble guanylyl cyclase mutants exhibit increased foraging locomotion: behavioral and genomic investigations. Behav. Genet. 35:231–44 55. Zayas RM, Trimmer BA. 2007. Characterization of NO/cGMP-mediated responses in identified mo- toneurons. Cell Mol. Neurobiol. 27:191–209 56. Wilson CH, Christensen TA, Nighorn AJ. 2007. Inhibition of nitric oxide and soluble guanylyl cyclase signaling affects olfactory neuron activity in the moth, Manduca sexta. J. Comp. Physiol. A 193:715–28 57. Fujie S, Yamamoto T, Murakami J, Hatakeyama D, Shiga H, et al. 2005. Nitric oxide synthase and soluble guanylyl cyclase underlying the modulation of electrical oscillations in a central olfactory organ. J. Neurobiol. 62:14–30 58. Gelperin A, Flores J, Raccuia-Behling F, Cooke IR. 2000. Nitric oxide and carbon monoxide modulate oscillations of olfactory interneurons in a terrestrial mollusk. J. Neurophysiol. 83:116–27 59. Cary SP, Winger JA, Derbyshire ER, Marletta MA. 2006. Nitric oxide signaling: no longer simply on or off. Trends Biochem. Sci. 31:231–39 60. Wedel B, Humbert P, Harteneck C, Foerster J, Malkewitz J, et al. 1994. Mutation of His-105 in the β1 subunit yields a nitric oxide-insensitive form of soluble guanylyl cyclase. Proc. Natl. Acad. Sci. USA 91:2592–96 Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org 61. Wedel B, Harteneck C, Foerster J, Friebe A, Schultz G, Koesling D. 1995. Functional domains of soluble guanylyl cyclase. J. Biol. Chem. 270:24871–75

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. 62. Iyer LM, Anantharaman V, Aravind L. 2003. Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins. BMC Genomics 4:5 63. Nioche P, Berka V, Vipond J, Minton N, Tsai AL, Raman CS. 2004. Femtomolar sensitivity of a NO sensor from Clostridium botulinum. Science 306:1550–53 64. Pellicena P, Karow DS, Boon EM, Marletta MA, Kuriyan J. 2004. Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases. Proc. Natl. Acad. Sci. USA 101:12854–59 65. Boon EM, Marletta MA. 2005. Ligand discrimination in soluble guanylate cyclase and the H-NOX family of heme sensor proteins. Curr. Opin. Chem. Biol. 9:441–46 66. Moglich A, Ayers RA, Moffat K. 2009. Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17:1282–94 67. Shiga T, Suzuki N. 2005. Amphipathic α-helix mediates the heterodimerization of soluble guanylyl cyclase. Zool. Sci. 22:735–42

554 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

68. Rothkegel C, Schmidt PM, Atkins DJ, Hoffmann LS, Schmidt HH, et al. 2007. Dimerization region of soluble guanylate cyclase characterized by bimolecular fluorescence complementation in vivo. Mol. Pharmacol. 72:1181–90 69. Ma X, Sayed N, Baskaran P, Beuve A, van den Akker F. 2008. PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure. J. Biol. Chem. 283:1167–78 70. Tesmer JJ, Sunahara RK, Gilman AG, Sprang SR. 1997. Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gsα ·GTPγS. Science 278:1907–16 71. Zhang G, Liu Y, Ruoho AE, Hurley JH. 1997. Structure of the adenylyl cyclase catalytic core. Nature 386:247–53 72. Sunahara RK, Beuve A, Tesmer JJ, Sprang SR, Garbers DL, Gilman AG. 1998. Exchange of substrate and inhibitor specificities between adenylyl and guanylyl cyclases. J. Biol. Chem. 273:16332–38 73. Brandwein HJ, Lewicki JA, Waldman SA, Murad F. 1982. Effect of GTP analogues on purified soluble guanylate cyclase. J. Biol. Chem. 257:1309–11 74. Garbers DL, Suddath JL, Hardman JG. 1975. Enzymatic formation of inosine 3,5-monophosphate and of 2-deoxyguanosine 3,5-monophosphate. Inosinate and deoxyguanylate cyclase activity. Biochim. Biophys. Acta 377:174–85 75. Gille A, Lushington GH, Mou TC, Doughty MB, Johnson RA, Seifert R. 2004. Differential inhibition of adenylyl cyclase isoforms and soluble guanylyl cyclase by purine and pyrimidine nucleotides. J. Biol. Chem. 279:19955–69 76. Derbyshire ER, Fernhoff NB, Deng S, Marletta MA. 2009. Nucleotide regulation of soluble guanylate cyclase substrate specificity. Biochemistry 48:7519–24 77. Haase T, Haase N, Kraehling JR, Behrends S. 2010. Fluorescent fusion proteins of soluble guanylyl cyclase indicate proximity of the heme nitric oxide domain and catalytic domain. PLoS ONE 5:e11617 78. Winger JA, Derbyshire ER, Lamers MH, Marletta MA, Kuriyan J. 2008. The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase. BMC Struct. Biol. 8:42 79. Rauch A, Leipelt M, Russwurm M, Steegborn C. 2008. Crystal structure of the guanylyl cyclase Cya2. Proc. Natl. Acad. Sci. USA 105:15720–25 80. Morton DB. 2004. Atypical soluble guanylyl cyclases in Drosophila can function as molecular oxygen sensors. J. Biol. Chem. 279:50651–53 81. Morton DB, Langlais KK, Stewart JA, Vermehren A. 2005. Comparison of the properties of the five soluble guanylyl cyclase subunits in Drosophila melanogaster. J. Insect Sci. 5:12 82. Huang SH, Rio DC, Marletta MA. 2007. Ligand binding and inhibition of an oxygen-sensitive soluble guanylate cyclase, Gyc-88E, from Drosophila. Biochemistry 46:15115–22 83. Vermehren-Schmaedick A, Ainsley JA, Johnson WA, Davies SA, Morton DB. 2010. Behavioral responses to hypoxia in Drosophila larvae are mediated by atypical soluble guanylyl cyclases. Genetics 186:183–96 84. Gray JM, Karow DS, Lu H, Chang AJ, Chang JS, et al. 2004. Oxygen sensation and social feeding mediated by a C. elegans guanylate cyclase homologue. Nature 430:317–22

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org 85. Cheung BH, Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate cyclases act in neurons exposed to the body ﬂuid to promote C. elegans aggregation behavior. Curr. Biol. 14:1105–11

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. 86. Cheung BH, Cohen M, Rogers C, Albayram O, de Bono M. 2005. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Curr. Biol. 15:905–17 87. Zimmer M, Gray JM, Pokala N, Chang AJ, Karow DS, et al. 2009. Neurons detect increases and decreases in oxygen levels using distinct guanylate cyclases. Neuron 61:865–79 88. Price MS, Chao LY, Marletta MA. 2007. Shewanella oneidensis MR-1 H-NOX regulation of a histidine kinase by nitric oxide. Biochemistry 46:13677–83 89. Wang Y, Dufour YS, Carlson HK, Donohue TJ, Marletta MA, Ruby EG. 2010. H-NOX-mediated nitric oxide sensing modulates symbiotic colonization by Vibrio ﬁscheri. Proc. Natl. Acad. Sci. USA 107:8375–80 90. Boon EM, Huang SH, Marletta MA. 2005. A molecular basis for NO selectivity in soluble guanylate cyclase. Nat. Chem. Biol. 1:53–59 91. Schmidt PM, Schramm M, Schroder H, Wunder F, Stasch JP. 2004. Identiﬁcation of residues crucially involved in the binding of the heme moiety of soluble guanylate cyclase. J. Biol. Chem. 279:3025–32

www.annualreviews.org • Structure and Regulation of SGC 555 BI81CH22-Marletta ARI 3 May 2012 12:17

92. Zhao Y, Schelvis JP, Babcock GT, Marletta MA. 1998. Identiﬁcation of histidine 105 in the β1 subunit of soluble guanylate cyclase as the heme proximal ligand. Biochemistry 37:4502–9 93. Ma X, Sayed N, Beuve A, van den Akker F. 2007. NO and CO differentially activate soluble guanylyl cyclase via a heme pivot-bend mechanism. EMBO J. 26:578–88 94. Erbil WK, Price MS, Wemmer DE, Marletta MA. 2009. A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation. Proc. Natl. Acad. Sci. USA 106:19753–60 95. Tran R, Boon EM, Marletta MA, Mathies RA. 2009. Resonance Raman spectra of an O2-binding H- NOX domain reveal heme relaxation upon mutation. Biochemistry 48:8568–77 96. Ibrahim M, Derbyshire ER, Marletta MA, Spiro TG. 2010. Probing soluble guanylate cyclase activation by CO and YC-1 using resonance Raman spectroscopy. Biochemistry 49:3815–23 97. Ibrahim M, Derbyshire ER, Soldatova AV, Marletta MA, Spiro TG. 2010. Soluble guanylate cyclase is activated differently by excess NO and by YC-1: resonance Raman spectroscopic evidence. Biochemistry 49:4864–71 98. Pal B, Tanaka K, Takenaka S, Kitagawa T. 2010. Resonance Raman spectroscopic investigation of structural changes of CO-heme in soluble guanylate cyclase generated by effectors and substrate. J. Raman Spectrosc. 41:1178–84 99. Olea C, Boon EM, Pellicena P, Kuriyan J, Marletta MA. 2008. Probing the function of heme distortion in the H-NOX family. ACS Chem. Biol. 3:703–10 100. Tsai AL, Berka V, Martin F, Ma X, van den Akker F, et al. 2010. Is Nostoc H-NOX a NO sensor or redox switch? Biochemistry 49:6587–99 101. Martin F, Baskaran P, Ma X, Dunten PW, Schaefer M, et al. 2010. Structure of cinaciguat (BAY 58-2667) bound to Nostoc H-NOX domain reveals insights into heme-mimetic activation of the soluble guanylyl cyclase. J. Biol. Chem. 285:22651–57 102. Barrick D. 1994. Replacement of the proximal ligand of sperm whale myoglobin with free imidazole in the mutant His-93→Gly. Biochemistry 33:6546–54 103. Evgenov OV, Pacher P, Schmidt PM, Hasko G, Schmidt HH, Stasch JP. 2006. NO-independent stimulators and activators of soluble guanylate cyclase: discovery and therapeutic potential. Nat. Rev. Drug Discov. 5:755–68 104. Baskaran P, Heckler EJ, van den Akker F, Beuve A. 2011. Aspartate 102 in the heme domain of soluble guanylyl cyclase has a key role in NO activation. Biochemistry 50:4291–97 105. Derbyshire ER, Deng S, Marletta MA. 2010. Incorporation of tyrosine and glutamine residues into the soluble guanylate cyclase heme distal pocket alters NO and O2 binding. J. Biol. Chem. 285:17471–78 106. Rothkegel C, Schmidt PM, Stoll F, Schroder H, Schmidt HHHW, Stasch JP. 2006. Identiﬁcation of residues crucially involved in soluble guanylate cyclase activation. FEBS Lett. 580:4205–13 107. Capece L, Estrin DA, Marti MA. 2008. Dynamical characterization of the heme NO oxygen binding (HNOX) domain. Insight into soluble guanylate cyclase allosteric transition. Biochemistry 47:9416–27 108. Xu C, Ibrahim M, Spiro TG. 2008. DFT analysis of axial and equatorial effects on heme-CO vibrational modes: applications to CooA and H-NOX heme sensor proteins. Biochemistry 47:2379–87 Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org 109. Makino R, Park SY, Obayashi E, Iizuka T, Hori H, Shiro Y. 2011. Oxygen binding and redox properties of the heme in soluble guanylate cyclase: implications for the mechanism of ligand discrimination.

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. J. Biol. Chem. 286:15678–87 110. Deinum G, Stone JR, Babcock GT, Marletta MA. 1996. Binding of nitric oxide and carbon monoxide to soluble guanylate cyclase as observed with resonance Raman spectroscopy. Biochemistry 35:1540–7 111. Jain R, Chan MK. 2003. Mechanisms of ligand discrimination by heme proteins. J. Biol. Inorg. Chem. 8:1–11 112. Zhang Y, Lu M, Cheng Y, Li Z. 2010. H-NOX domains display different tunnel systems for ligand migration. J. Mol. Graph. Model. 28:814–19 113. Winter MB, Herzik MA, Kuriyan J, Marletta MA. 2011. Tunnels modulate ligand ﬂux in a heme nitric oxide/oxygen binding (H-NOX) domain. Proc. Natl. Acad. Sci. USA. 108:E881–89 114. Martin E, Berka V, Bogatenkova E, Murad F, Tsai AL. 2006. Ligand selectivity of soluble guanylyl cyclase: effect of the hydrogen-bonding tyrosine in the distal heme pocket on binding of oxygen, nitric oxide, and carbon monoxide. J. Biol. Chem. 281:27836–45

556 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

115. Das TK, Samuni U, Lin Y, Goldberg DE, Rousseau DL, Friedman JM. 2004. Distal heme pocket conformers of carbonmonoxy derivatives of Ascaris hemoglobin: evidence of conformational trapping in porous sol-gel matrices. J. Biol. Chem. 279:10433–41 116. Giangiacomo L, Ilari A, Boffi A, Morea V, Chiancone E. 2005. The truncated oxygen-avid hemoglobin from Bacillus subtilis: X-ray structure and ligand binding properties. J. Biol. Chem. 280:9192–202 117. Marti MA, Capece L, Bikiel DE, Falcone B, Estrin DA. 2007. Oxygen affinity controlled by dynamical distal conformations: the soybean leghemoglobin and the Paramecium caudatum hemoglobin cases. Proteins 68:480–87 118. Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, et al. 2004. Heme-ligand tunneling in group I truncated hemoglobins. J. Biol. Chem. 279:21520–25 119. Schrammel A, Behrends S, Schmidt K, Koesling D, Mayer B. 1996. Characterization of 1H- [1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one as a heme-site inhibitor of nitric oxide-sensitive guanylyl cyclase. Mol. Pharmacol. 50:1–5 120. Stone JR, Marletta MA. 1996. Spectral and kinetic studies on the activation of soluble guanylate cyclase by nitric oxide. Biochemistry 35:1093–99 121. Bellamy TC, Garthwaite J. 2001. Sub-second kinetics of the nitric oxide receptor, soluble guanylyl cyclase, in intact cerebellar cells. J. Biol. Chem. 276:4287–92 122. Cary SP, Winger JA, Marletta MA. 2005. Tonic and acute nitric oxide signaling through soluble guanylate cyclase is mediated by nonheme nitric oxide, ATP, and GTP. Proc. Natl. Acad. Sci. USA 102:13064–69 123. Russwurm M, Koesling D. 2004. NO activation of guanylyl cyclase. EMBO J. 23:4443–50 124. Derbyshire ER, Gunn A, Ibrahim M, Spiro TG, Britt RD, Marletta MA. 2008. Characterization of two different five-coordinate soluble guanylate cyclase ferrous-nitrosyl complexes. Biochemistry 47:3892–99 125. Fernhoff NB, Derbyshire ER, Marletta MA. 2009. A nitric oxide/cysteine interaction mediates the activation of soluble guanylate cyclase. Proc. Natl. Acad. Sci. USA 106:21602–7 126. Lawson DM, Stevenson CE, Andrew CR, Eady RR. 2000. Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase. EMBO J. 19:5661–71 127. Roy B, Garthwaite J. 2006. Nitric oxide activation of guanylyl cyclase in cells revisited. Proc. Natl. Acad. Sci. USA 103:12185–90 128. Palmer RM, Ferrige AG, Moncada S. 1987. Nitric oxide release accounts for the biological activity of endothelium-derived relaxing factor. Nature 327:524–26 129. Margulis A, Sitaramayya A. 2000. Rate of deactivation of nitric oxide-stimulated soluble guanylate cyclase: influence of nitric oxide scavengers and calcium. Biochemistry 39:1034–39 130. Russwurm M, Mergia E, Mullershausen F, Koesling D. 2002. Inhibition of deactivation of NO-sensitive guanylyl cyclase accounts for the sensitizing effect of YC-1. J. Biol. Chem. 277:24883–88 131. Kharitonov VG, Russwurm M, Magde D, Sharma VS, Koesling D. 1997. Dissociation of nitric oxide from soluble guanylate cyclase. Biochem. Biophys. Res. Commun. 239:284–86 132. Bellamy TC, Wood J, Goodwin DA, Garthwaite J. 2000. Rapid desensitization of the nitric oxide

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org receptor, soluble guanylyl cyclase, underlies diversity of cellular cGMP responses. Proc. Natl. Acad. Sci. USA 97:2928–33 133. Schroder H, Leitman DC, Bennett BM, Waldman SA, Murad F. 1988. Glyceryl trinitrate-induced Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. desensitization of guanylate cyclase in cultured rat lung ﬁbroblasts. J. Pharmacol. Exp. Ther. 245:413–18 134. Elkayam U, Kulick D, McIntosh N, Roth A, Hsueh W, Rahimtoola SH. 1987. Incidence of early tolerance to hemodynamic effects of continuous infusion of nitroglycerin in patients with coronary artery disease and heart failure. Circulation 76:577–84 135. Kim D, Rybalkin SD, Pi X, Wang Y, Zhang C, et al. 2001. Upregulation of phosphodiesterase 1A1 expression is associated with the development of nitrate tolerance. Circulation 104:2338–43 136. Sydow K, Daiber A, Oelze M, Chen Z, August M, et al. 2004. Central role of mitochondrial aldehyde dehydrogenase and reactive oxygen species in nitroglycerin tolerance and cross-tolerance. J. Clin. Investig. 113:482–89 137. Sayed N, Baskaran P, Ma X, van den Akker F, Beuve A. 2007. Desensitization of soluble guanylyl cyclase, the NO receptor, by S-nitrosylation. Proc. Natl. Acad. Sci. USA 104:12312–17

www.annualreviews.org • Structure and Regulation of SGC 557 BI81CH22-Marletta ARI 3 May 2012 12:17

138. Sayed N, Kim DD, Fioramonti X, Iwahashi T, Duran WN, Beuve A. 2008. Nitroglycerin-induced S- nitrosylation and desensitization of soluble guanylyl cyclase contribute to nitrate tolerance. Circ. Res. 103:606–14 139. Brandwein HJ, Lewicki JA, Murad F. 1981. Reversible inactivation of guanylate cyclase by mixed disulﬁde formation. J. Biol. Chem. 256:2958–62 140. Maron BA, Zhang YY, Handy DE, Beuve A, Tang SS, et al. 2009. Aldosterone increases oxidant stress to impair guanylyl cyclase activity by cysteinyl thiol oxidation in vascular smooth muscle cells. J. Biol. Chem. 284:7665–72 141. Derbyshire ER, Marletta MA. 2007. Butyl isocyanide as a probe of the activation mechanism of soluble guanylate cyclase. Investigating the role of non-heme nitric oxide. J. Biol. Chem. 282:35741–48 142. Derbyshire ER, Tran R, Mathies RA, Marletta MA. 2005. Characterization of nitrosoalkane binding and activation of soluble guanylate cyclase. Biochemistry 44:16257–65 143. Makino R, Matsuda H, Obayashi E, Shiro Y, Iizuka T, Hori H. 1999. EPR characterization of axial bond in metal center of native and cobalt-substituted guanylate cyclase. J. Biol. Chem. 274:7714–23 144. Ko FN, Wu CC, Kuo SC, Lee FY, Teng CM. 1994. YC-1, a novel activator of platelet guanylate cyclase. Blood 84:4226–33 145. Friebe A, Schultz G, Koesling D. 1996. Sensitizing soluble guanylyl cyclase to become a highly CO- sensitive enzyme. EMBO J. 15:6863–68 146. Stone JR, Marletta MA. 1998. Synergistic activation of soluble guanylate cyclase by YC-1 and carbon monoxide: implications for the role of cleavage of the iron-histidine bond during activation by nitric oxide. Chem. Biol. 5:255–61 147. Makino R, Obayashi E, Homma N, Shiro Y, Hori H. 2003. YC-1 facilitates release of the proximal His residue in the NO and CO complexes of soluble guanylate cyclase. J. Biol. Chem. 278:11130–37 148. Stasch JP, Becker EM, Alonso-Alija C, Apeler H, Dembowsky K, et al. 2001. NO-independent regulatory site on soluble guanylate cyclase. Nature 410:212–15 149. Friebe A, Russwurm M, Mergia E, Koesling D. 1999. A point-mutated guanylyl cyclase with features of the YC-1-stimulated enzyme: implications for the YC-1 binding site? Biochemistry 38:15253–57 150. Lamothe M, Chang FJ, Balashova N, Shirokov R, Beuve A. 2004. Functional characterization of nitric oxide and YC-1 activation of soluble guanylyl cyclase: structural implication for the YC-1 binding site? Biochemistry 43:3039–48 151. Yazawa S, Tsuchiya H, Hori H, Makino R. 2006. Functional characterization of two nucleotide-binding sites in soluble guanylate cyclase. J. Biol. Chem. 281:21763–70 152. Kharitonov VG, Sharma VS, Magde D, Koesling D. 1999. Kinetics and equilibria of soluble guanylate cyclase ligation by CO: effect of YC-1. Biochemistry 38:10699–706 153. Denninger JW, Schelvis JP, Brandish PE, Zhao Y, Babcock GT, Marletta MA. 2000. Interaction of soluble guanylate cyclase with YC-1: kinetic and resonance Raman studies. Biochemistry 39:4191–98 154. Sharma VS, Magde D, Kharitonov VG, Koesling D. 1999. Soluble guanylate cyclase: effect of YC-1 on ligation kinetics with carbon monoxide. Biochem. Biophys. Res. Commun. 254:188–91 155. Bischoff E, Stasch JP. 2004. Effects of the sGC stimulator BAY 41-2272 are not mediated by phospho- Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org diesterase 5 inhibition. Circulation 110:e320–21; author reply e20–1 156. Mullershausen F, Russwurm M, Friebe A, Koesling D. 2004. Inhibition of phosphodiesterase type 5 by

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. the activator of nitric oxide-sensitive guanylyl cyclase BAY 41-2272. Circulation 109:1711–13 157. Belik J. 2009. Riociguat, an oral soluble guanylate cyclase stimulator for the treatment of pulmonary hypertension. Curr. Opin. Investig. Drugs 10:971–79 158. Stasch JP, Schmidt P, Alonso-Alija C, Apeler H, Dembowsky K, et al. 2002. NO- and haem-independent activation of soluble guanylyl cyclase: molecular basis and cardiovascular implications of a new pharmacological principle. Br. J. Pharmacol. 136:773–83 159. Roy B, Mo E, Vernon J, Garthwaite J. 2008. Probing the presence of the ligand-binding haem in cellular nitric oxide receptors. Br.J.Pharmacol.153:1495–504 160. Meurer S, Pioch S, Pabst T, Opitz N, Schmidt PM, et al. 2009. Nitric oxide-independent vasodilator rescues heme-oxidized soluble guanylate cyclase from proteasomal degradation. Circ. Res. 105:33–41 161. Kalk P, Godes M, Relle K, Rothkegel C, Hucke A, et al. 2006. NO-independent activation of soluble guanylate cyclase prevents disease progression in rats with 5/6 nephrectomy. Br. J. Pharmacol. 148:853–59

558 Derbyshire · Marletta BI81CH22-Marletta ARI 3 May 2012 12:17

162. Korkmaz S, Radovits T, Barnucz E, Hirschberg K, Neugebauer P, et al. 2009. Pharmacological activation of soluble guanylate cyclase protects the heart against ischemic injury. Circulation 120:677–86 163. Frey R, Muck W, Unger S, Artmeier-Brandt U, Weimann G, Wensing G. 2008. Pharmacokinetics, pharmacodynamics, tolerability, and safety of the soluble guanylate cyclase activator cinaciguat (BAY 58-2667) in healthy male volunteers. J. Clin. Pharmacol. 48:1400–10 164. Lapp H, Mitrovic V, Franz N, Heuer H, Buerke M, et al. 2009. Cinaciguat (BAY 58-2667) improves car- diopulmonary hemodynamics in patients with acute decompensated heart failure. Circulation 119:2781– 88 165. Mueck W, Frey R. 2010. Population pharmacokinetics and pharmacodynamics of cinaciguat, a soluble guanylate cyclase activator, in patients with acute decompensated heart failure. Clin. Pharmacokinet. 49:119–29 166. Garthwaite J, Southam E, Boulton CL, Nielsen EB, Schmidt K, Mayer B. 1995. Potent and selective inhibition of nitric oxide-sensitive guanylyl cyclase by 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one. Mol. Pharmacol. 48:184–88 167. Mulsch A, Busse R, Liebau S, Forstermann U. 1988. LY 83583 interferes with the release of endothelium- derived relaxing factor and inhibits soluble guanylate cyclase. J. Pharmacol. Exp. Ther. 247:283–88 168. Gruetter CA, Kadowitz PJ, Ignarro LJ. 1981. Methylene blue inhibits coronary arterial relaxation and guanylate cyclase activation by nitroglycerin, sodium nitrite, and amyl nitrite. Can. J. Physiol. Pharmacol. 59:150–56 169. Lee YS, Wurster RD. 1995. Mechanism of potentiation of LY83583-induced growth inhibition by sodium nitroprusside in human brain tumor cells. Cancer Chemother. Pharmacol. 36:341–44 170. Wolin MS, Cherry PD, Rodenburg JM, Messina EJ, Kaley G. 1990. Methylene blue inhibits vasodilation of skeletal muscle arterioles to acetylcholine and nitric oxide via the extracellular generation of superoxide anion. J. Pharmacol. Exp. Ther. 254:872–76 171. Chang FJ, Lemme S, Sun Q, Sunahara RK, Beuve A. 2005. Nitric oxide-dependent allosteric inhibitory role of a second nucleotide binding site in soluble guanylyl cyclase. J. Biol. Chem. 280:11513–19 172. Suzuki T, Suematsu M, Makino R. 2001. Organic phosphates as a new class of soluble guanylate cyclase inhibitors. FEBS Lett. 507:49–53 Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only.

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Annual Review of Biochemistry Contents Volume 81, 2012

Preface Preface and Dedication to Christian R.H. Raetz JoAnne Stubbe ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppxi

Prefatories A Mitochondrial Odyssey Walter Neupert pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp1 The Fires of Life Gottfried Schatz pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp34

Chromatin, Epigenetics, and Transcription Theme Introduction to Theme “Chromatin, Epigenetics, and Transcription” Joan W. Conaway pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp61 The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis Ali Shilatifard pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp65 Programming of DNA Methylation Patterns Howard Cedar and Yehudit Bergman ppppppppppppppppppppppppppppppppppppppppppppppppppppppp97 RNA Polymerase II Elongation Control Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org Qiang Zhou, Tiandao Li, and David H. Price pppppppppppppppppppppppppppppppppppppppppppp119

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. Genome Regulation by Long Noncoding RNAs John L. Rinn and Howard Y. Chang pppppppppppppppppppppppppppppppppppppppppppppppppppppp145

Protein Tagging Theme The Ubiquitin System, an Immense Realm Alexander Varshavsky pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp167 Ubiquitin and Proteasomes in Transcription Fuqiang Geng, Sabine Wenzel, and William P. Tansey ppppppppppppppppppppppppppppppppp177

v BI81-FrontMatter ARI 9 May 2012 7:26

The Ubiquitin Code David Komander and Michael Rape ppppppppppppppppppppppppppppppppppppppppppppppppppppppp203 Ubiquitin and Membrane Protein Turnover: From Cradle to Grave Jason A. MacGurn, Pi-Chiang Hsu, and Scott D. Emr ppppppppppppppppppppppppppppppppp231 The N-End Rule Pathway Takafumi Tasaki, Shashikanth M. Sriram, Kyong Soo Park, and Yong Tae Kwon ppp261 Ubiquitin-Binding Proteins: Decoders of Ubiquitin-Mediated Cellular Functions Koraljka Husnjak and Ivan Dikic ppppppppppppppppppppppppppppppppppppppppppppppppppppppppp291 Ubiquitin-Like Proteins Annemarthe G. van der Veen and Hidde L. Ploegh pppppppppppppppppppppppppppppppppppppp323

Recent Advances in Biochemistry Toward the Single-Hour High-Quality Genome Patrik L. Sta˚hl and Joakim Lundeberg ppppppppppppppppppppppppppppppppppppppppppppppppppp359 Mass Spectrometry–Based Proteomics and Network Biology Ariel Bensimon, Albert J.R. Heck, and Ruedi Aebersold ppppppppppppppppppppppppppppppppp379 Membrane Fission: The Biogenesis of Transport Carriers Felix Campelo and Vivek Malhotra ppppppppppppppppppppppppppppppppppppppppppppppppppppppp407 Emerging Paradigms for Complex Iron-Sulfur Cofactor Assembly and Insertion John W. Peters and Joan B. Broderick pppppppppppppppppppppppppppppppppppppppppppppppppppp429 Structural Perspective of Peptidoglycan Biosynthesis and Assembly Andrew L. Lovering, Susan S. Safadi, and Natalie C.J. Strynadka pppppppppppppppppppp451 Discovery, Biosynthesis, and Engineering of Lantipeptides Patrick J. Knerr and Wilfred A. van der Donk pppppppppppppppppppppppppppppppppppppppppp479 Regulation of Glucose Transporter Translocation Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org in Health and Diabetes Jonathan S. Bogan pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp507 Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. Structure and Regulation of Soluble Guanylate Cyclase Emily R. Derbyshire and Michael A. Marletta ppppppppppppppppppppppppppppppppppppppppppp533 The MPS1 Family of Protein Kinases Xuedong Liu and Mark Winey pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp561 The Structural Basis for Control of Eukaryotic Protein Kinases Jane A. Endicott, Martin E.M. Noble, and Louise N. Johnson pppppppppppppppppppppppppp587

vi Contents BI81-FrontMatter ARI 9 May 2012 7:26

Measurements and Implications of the Membrane Dipole Potential Liguo Wang ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp615 GTPase Networks in Membrane Trafﬁc Emi Mizuno-Yamasaki, Felix Rivera-Molina, and Peter Novick ppppppppppppppppppppppp637 Roles for Actin Assembly in Endocytosis Olivia L. Mooren, Brian J. Galletta, and John A. Cooper ppppppppppppppppppppppppppppppp661 Lipid Droplets and Cellular Lipid Metabolism Tobias C. Walther and Robert V. Farese Jr. pppppppppppppppppppppppppppppppppppppppppppppp687 Adipogenesis: From Stem Cell to Adipocyte Qi Qun Tang and M. Daniel Lane pppppppppppppppppppppppppppppppppppppppppppppppppppppppp715 Pluripotency and Nuclear Reprogramming Marion Dejosez and Thomas P. Zwaka ppppppppppppppppppppppppppppppppppppppppppppppppppp737 Endoplasmic Reticulum Stress and Type 2 Diabetes Sung Hoon Back and Randal J. Kaufman pppppppppppppppppppppppppppppppppppppppppppppppp767 Structure Uniﬁes the Viral Universe Nicola G.A. Abrescia, Dennis H. Bamford, Jonathan M. Grimes, and David I. Stuart pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp795

Indexes Cumulative Index of Contributing Authors, Volumes 77–81 ppppppppppppppppppppppppppp823 Cumulative Index of Chapter Titles, Volumes 77–81 ppppppppppppppppppppppppppppppppppp827

Errata An online log of corrections to Annual Review of Biochemistry articles may be found at http://biochem.annualreviews.org/errata.shtml Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only.

Contents vii Annual Reviews It’s about time. Your time. It’s time well spent.

New From Annual Reviews: Annual Review of Statistics and Its Application Volume 1 • Online January 2014 • http://statistics.annualreviews.org Editor: Stephen E. Fienberg, Carnegie Mellon University Associate Editors: Nancy Reid, University of Toronto Stephen M. Stigler, University of Chicago The Annual Review of Statistics and Its Application aims to inform statisticians and quantitative methodologists, as well as all scientists and users of statistics about major methodological advances and the computational tools that allow for their implementation. It will include developments in the field of statistics, including theoretical statistical underpinnings of new methodology, as well as developments in specific application domains such as biostatistics and bioinformatics, economics, machine learning, psychology, sociology, and aspects of the physical sciences. Complimentary online access to the first volume will be available until January 2015.

table of contents: • What Is Statistics? Stephen E. Fienberg • High-Dimensional Statistics with a View Toward Applications • A Systematic Statistical Approach to Evaluating Evidence in Biology, Peter Bühlmann, Markus Kalisch, Lukas Meier from Observational Studies, David Madigan, Paul E. Stang, • Next-Generation Statistical Genetics: Modeling, Penalization, Jesse A. Berlin, Martijn Schuemie, J. Marc Overhage, and Optimization in High-Dimensional Data, Kenneth Lange, Marc A. Suchard, Bill Dumouchel, Abraham G. Hartzema, Jeanette C. Papp, Janet S. Sinsheimer, Eric M. Sobel Patrick B. Ryan • Breaking Bad: Two Decades of Life-Course Data Analysis • The Role of Statistics in the Discovery of a Higgs Boson, in Criminology, Developmental Psychology, and Beyond, David A. van Dyk Elena A. Erosheva, Ross L. Matsueda, Donatello Telesca • Brain Imaging Analysis, F. DuBois Bowman • Event History Analysis, Niels Keiding • Statistics and Climate, Peter Guttorp • Statistical Evaluation of Forensic DNA Profile Evidence, • Climate Simulators and Climate Projections, Christopher D. Steele, David J. Balding Jonathan Rougier, Michael Goldstein • Using League Table Rankings in Public Policy Formation: • Probabilistic Forecasting, Tilmann Gneiting, Statistical Issues, Harvey Goldstein Matthias Katzfuss • Statistical Ecology, Ruth King

Annu. Rev. Biochem. 2012.81:533-559. Downloaded from www.annualreviews.org • Bayesian Computational Tools, Christian P. Robert • Estimating the Number of Species in Microbial Diversity • Bayesian Computation Via Markov Chain Monte Carlo, Studies, John Bunge, Amy Willis, Fiona Walsh

Access provided by b-on: Universidade Nova de Lisboa (UNL) on 01/18/15. For personal use only. Radu V. Craiu, Jeffrey S. Rosenthal • Dynamic Treatment Regimes, Bibhas Chakraborty, • Build, Compute, Critique, Repeat: Data Analysis with Latent Susan A. Murphy Variable Models, David M. Blei • Statistics and Related Topics in Single-Molecule Biophysics, • Structured Regularizers for High-Dimensional Problems: Hong Qian, S.C. Kou Statistical and Computational Issues, Martin J. Wainwright • Statistics and Quantitative Risk Management for Banking and Insurance, Paul Embrechts, Marius Hofert

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