ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster Jae-Hun Jeounga and Holger Dobbeka,1 aInstitut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 2, 2018 (received for review November 23, 2017) Chemically demanding reductive conversions in biology, such as the We have characterized the two components of a widespread reduction of dinitrogen to ammonia or the Birch-type reduction of system of the third type and find that the electron-accepting – aromatic compounds, depend on Fe/S-cluster containing ATPases. component features a double-cubane [Fe8S9]-cluster. This [Fe8S9]- These reductions are typically catalyzed by two-component systems, cluster, so far unknown to biology, catalyzes reductive reactions in which an Fe/S-cluster–containing ATPase energizes an electron to otherwise associated only with the complex iron–sulfur clusters reduce a metal site on the acceptor protein that drives the reductive of nitrogenases. Our results reveal several parallels between the reaction. Here, we show a two-component system featuring a double-cubane cluster-containing enzymes and nitrogenases μ double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2( 2-S)]. The double- and suggest that an unexplored biochemical reactivity space cubane–cluster-containing enzyme is capable of reducing small mol- may be hidden among the diverse ATP-dependent two-component − ecules, such as acetylene (C2H2), azide (N3 ), and hydrazine (N2H4). enzymes. We thus present a class of metalloenzymes akin in fold, metal clus- ters, and reactivity to nitrogenases. Results Distribution of Double-Cubane Cluster Protein-Like Proteins. We ana- Fe/S-cluster | nitrogenase | acetylene | ATPase | electron transfer lyzedInterProentryIPR010327(https://www.ebi.ac.uk/interpro/) that includes the protein families of benzoyl-CoA reductase B/C iological redox reactions occur at a wide spectrum of re- subunit (BcrB/C) and dehydratase α/β subunit (HadB/C). Se- Bduction potentials. Some vital reactions take place at the quences of this entry are widely distributed and found in the BIOCHEMISTRY perimeters of reduction potentials achievable in water, extending genome of various bacteria and archaea, including firmicutes, biological reactivity space to the limits set by the environment. spirochaetes, actinobacteria, enterobacteria, deltaproteobacteria, Among these reactions are central processes, such as the oxi- and euryarchaeota. A sequence similarity network analysis of dation of water to dioxygen or the reduction of dinitrogen to all 1,436 sequences reveals potential separation into five larger ammonia. These and related biochemical reactions are out- clusters (Fig. 1). Cluster I includes proteins of varying length standing for two reasons: first they are coupled to energy- (420 and 1,800 aa), where the longer proteins appear to be fusions converting reactions in which light energy or the chemical energy between a dehydratase-type α/β unit and an ATP-dependent ac- stored in ATP are converted into reactive electrons/electron tivator. Cluster I may be subdivided into three major subclusters, holes, and second they occur at complex metal clusters, together distinguished by length and number of conserved Cys-motifs enabling valuable chemical transformations. (Fig. 1). Sequences in cluster II are ∼380 aa long and contain ATP-driven redox reactions are typically catalyzed by enzymes the α-subunits of benzoyl-CoA reductases (BcrC O87874) and consisting of two components. The first component is an ATPase containing an Fe/S-cluster on which the electron to be trans- Significance ferred is resting. The second component, also a metalloenzyme, is the electron acceptor in need of a highly energetic electron Our ability to reduce stable small molecules, such as dinitrogen because it contains one or more metal centers, which cannot be or carbon dioxide, is as vital as it is demanding and requires reduced at physiological reduction potentials. Three principal energetic electrons and a catalyst. In nature, these require- classes of electron-energizing ATPases are currently known: the ments are met by two-component enzymes: an electron- nitrogenase-like proteins, the RACE (reductive activator of donating metallo-ATPase and the principal catalyst, a metal- corrinoid enzymes)-type activators, and the benzoyl-CoA re- – loprotein with a low-potential cofactor. Here, we present a ductase/atypical dehydratase activators (1 3). The nitrogenase two-component enzyme in which the catalyst houses a double- system represents the most extensively studied example for ATP- cubane type [Fe8S9]-cluster. Iron–sulfur clusters with so high dependent electron transfer, not only because it was discovered nuclearity were so far only known from nitrogenase, an en- first, but also because of the relevance of biological dinitrogen – zyme notorious for its capacity to reduce various small mole- fixation and its parallels to the Haber Bosch process. Addi- cules. The enzyme not only shares structural features with tionally, nitrogenases catalyze several nonphysiological reduc- nitrogenase, but is also able to reduce acetylene, indicating its tions, including the potentially very useful reduction and C-C potential employment for reductive reactions of our choice. coupling of CO to small hydrocarbons, opening the field to new – applications (4 9). Moreover, homologs of nitrogenases act in Author contributions: J.-H.J. and H.D. designed research; J.-H.J. performed research; J.-H.J. different branches of tetrapyrroll biosynthesis, indicating that the and H.D. analyzed data; and J.-H.J. and H.D. wrote the paper. same type of ATPase-coupled electron transfer may be used for The authors declare no conflict of interest. very different chemical reactions (1, 10, 11). RACE-type acti- This article is a PNAS Direct Submission. vators reduce corrinoid-containing enzymes, which are difficult Published under the PNAS license. to reductively reactivate once they drop into the inactive Co(II) Data deposition: The atomic coordinates and structure factors have been deposited in the oxidation state (2, 12, 13). Finally, there are the ATPases driving Protein Data Bank, www.wwpdb.org (PDB ID code 6ENO). electron transfers to reduce benzoyl-CoA or to trigger an atyp- 1To whom correspondence should be addressed. Email: [email protected] ical β,α-dehydration of 2-hydroxyacyl-CoA esters (3). These berlin.de. ATPases share with the first group the general architecture, with This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. an [Fe4S4]-cluster placed in the dimer interface, likely triggering 1073/pnas.1720489115/-/DCSupplemental. electron transfer by conformational changes. www.pnas.org/cgi/doi/10.1073/pnas.1720489115 PNAS Latest Articles | 1of6 Downloaded by guest on September 25, 2021 the spectrum of DCCPCh did not change, indicating a very low reduction potential for the Fe/S-cluster on DCCPCh. The Fe/S-cluster on DCCPCh can be reduced by DT-reduced DCCP-RCh upon ATP-addition (Fig. 2B). When we add 2 mM Mg-ATP in the presence of prereduced DCCP-RCh, absorption of DCCPCh (1.6:1 = DCCP-RCh:DCCPCh) around 420 nm de- creases. We approximated the absorbance change at 420 nm by a monoexponential function with an observed rate constant of −1 0.66 min at 25 °C. When DCCP-RCh was supplied sub- stoichiometrically (0.5:1 = DCCP-RCh:DCCPCh), we observed a similar amplitude, but substantially slower reduction, indicating the same extent of DCCPCh reduction at lower rate. Next, we examined the ATP hydrolysis activity of DCCP-RCh. The ATPase activity of DCCP-RCh was determined at different conditions (Fig. S1A). The ATPase activity of oxidized DCCP- −1 RCh is 30 ± 1.8 nmol/min/mgDCCP-R (kobs = 0.84 min )at35°C and was not changed when DCCP-RCh was reduced with DT. In contrast, when DCCPCh was present in the assay buffer, the ATPase activity increased almost threefold (83.2 ± 5.3 nmol/min/ −1 mgDCCP-R; kobs = 2.4 min , n = 3). We tested the reductase activity of DCCPCh by following its ability to reduce acetylene. Acetylene reduction was strictly Fig. 1. Sequence similarity analysis. InterPro entry IPR010327 was analyzed using the EFI-EST server (36) with an alignment score of 20, visualized with Cytoscape (v3.3.0) (37) and colored by protein length (color code below). Distinct clusters (I−V) are indicated together with the number of conserved cysteine residues. the β-subunits of atypical dehydratases (HadC Q5U923), whose catalytic partner-subunits (BcrB O87875; HadB Q5U924), usually ∼410–430 aa, are clearly separated into cluster III. Both clusters II and III share a conserved 3-Cys motif, binding an [Fe4S4]-cluster with one open coordination site (14). Cluster IV contains proteins with 380–420 aa. Regardless of protein length, all sequences of cluster IV share a highly conserved 7-Cys motif (CX19CX18–19CX29CX166–170CX32–34CX32C) (Fig. S3B). A small isolatedcluster(clusterV)featuresproteinswith∼330 aa sharing a strictly conserved 3-Cys motif. We investigated the properties of a 7-Cys-protein from cluster IV, encoded by CHY_0487 from Carboxydothermus hydrogenoformans Z-2901. In contrast to the 2-hydroxyacyl-CoA dehydratases and benzoyl-CoA reductases, which are encoded by two homologous genes forming α/β-dimers, no homologous protein is found near CHY_0487. Instead, CHY_0487 is located in an operon with only one other gene (CHY_0488), annotated to encode an ATP- dependent