DOCSLIB.ORG

Tryptophan Synthase Complexes: Evolution, Substrate Specificity, and Quaternary Structure

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Tryptophan Synthase Complexes: Evolution, Substrate Specificity, and Quaternary Structure Tryptophan Synthase Complexes: Evolution, Substrate Specificity, and Quaternary Structure DISSERTATION ZUR ERLANGUNG DES DOKTORGRADES DER NATURWISSENSCHAFTEN (DR. RER. NAT.) DER FAKULTÄT FÜR BIOLOGIE UND VORKLINISCHE MEDIZIN DER UNIVERSITÄT REGENSBURG vorgelegt von Florian Busch aus Kösching im Jahr 2015 Das Promotionsgesuch wurde eingereicht am: 29.5.2015 Die Arbeit wurde angeleitet von: Prof. Dr. Reinhard Sterner Unterschrift: This work was done in the period from November 2010 to May 2015 in the group of Prof. Dr. Reinhard Sterner (Biochemistry II, Institute of Biophysics and Physical Biochemistry, University of Regensburg). ‘It is apparent that our knowledge of the structure and function of this enzyme [the tryptophan synthase complex] is providing a glimpse of the sophistication that is feasible in natural protein design.’ Edith Miles TABLE OF CONTENTS I TABLE OF CONTENTS TABLE OF CONTENTS ............................................................................................... I LIST OF FIGURES ..................................................................................................... V LIST OF TABLES .................................................................................................... VII FORMULA INDEX .................................................................................................. VIII LIST OF COMMON USED ABBREVIATIONS ......................................................... IX PREFACE ................................................................................................................... 1 1 EVOLUTION OF THE PERMANENT TS ............................................................... 2 1.1 Introduction ................................................................................................................... 2 1.1.1 The heterotetrameric tryptophan synthase complex.......................................... 2 1.1.2 Catalyzed reactions ........................................................................................... 2 1.1.3 The reaction at the α-subunit ............................................................................. 3 1.1.4 The reaction at the β-subunit ............................................................................. 3 1.1.5 Subunits and subunit assembly ......................................................................... 4 1.1.6 Allostery within the TS ....................................................................................... 5 1.1.7 The TS as model system ................................................................................... 9 1.1.8 Ancestral protein reconstruction ...................................................................... 10 1.2 Remarks ....................................................................................................................... 10 1.3 Significance of this work ............................................................................................ 10 1.4 Results and discussion .............................................................................................. 12 1.4.1 Reconstruction of an ancient LCA TS.............................................................. 12 1.4.2 Cloning of LCA subunits .................................................................................. 13 1.4.3 Expression and purification of LCA subunits ................................................... 14 1.4.4 Structural integrity, thermal stability, and activity of LCA subunits .................. 15 1.4.5 Subunit assembly and activity of subunits within the LCA TS ......................... 17 1.4.6 Impairment of the β-reaction within the LCA TS .............................................. 20 1.4.7 Allosteric communication within the LCA TS ................................................... 23 1.4.8 Substrate channeling within the LCA TS ......................................................... 24 1.5 Conclusion .................................................................................................................. 26 1.6 Ongoing research and future work ........................................................................... 28 2 SUBSTRATE SPECIFICITY OF β-SUBUNIT HOMOLOGS ............................... 29 2.1 Introduction ................................................................................................................. 29 2.1.1 Phylogenetic analysis of the TrpB enzyme family ........................................... 29 2.1.2 Abundance and properties of TrpB2 enzymes ................................................ 30 2.1.3 Hypothesis on the function of TrpB2 enzymes ................................................ 31 2.2 Remarks ....................................................................................................................... 31 2.3 Significance of this work ............................................................................................ 31 2.4 Results and discussion .............................................................................................. 33 2.4.1 Phylogenetic distribution of TrpB1 and TrpB2 enzymes .................................. 33 2.4.2 Comparison of conserved residues in TrpB1 and TrpB2 enzymes ................. 34 2.4.3 Cloning of TrpB1 and TrpB2 enzymes............................................................. 35 2.4.4 Expression and purification of TrpB1 and TrpB2 enzymes.............................. 36 2.4.5 Screen for the synthesis of β-substituted tryptophans ..................................... 37 2.4.6 Screen for the synthesis of tryptophan ............................................................ 38 II TABLE OF CONTENTS 2.4.7 Crystallization of ssTrpB2a .............................................................................. 40 2.4.8 Structure of ssTrpB2a with bound OPS ........................................................... 41 2.4.9 Cloning of TrpB2 variants ................................................................................ 43 2.4.10 Expression and purification of TrpB2 variants ................................................. 44 2.4.11 Binding properties of TrpB2 variants ................................................................ 44 2.4.12 Divergent evolution in the cystein synthase family .......................................... 45 2.5 Conclusion ................................................................................................................... 46 3 THE QUATERNARY STRUCTURE OF TRANSIENT TS ................................... 48 3.1 Introduction ................................................................................................................. 48 3.1.1 Structure of the permanent TS ......................................................................... 48 3.1.2 Structure of the transient TS ............................................................................ 49 3.1.3 The non-interacting enzyme ssTrpB2a ............................................................ 50 3.2 Remarks ....................................................................................................................... 50 3.3 Significance of this work ............................................................................................ 50 3.4 Results and discussion .............................................................................................. 52 3.4.1 Cloning of subunits of a transient and a permanent TS ................................... 52 3.4.2 Expression and purification of subunits of a transient and a permanent TS .... 52 3.4.3 Influence of different ligands on the transient TS ............................................. 53 3.4.4 Channeling within the transient TS .................................................................. 55 3.4.5 Phylogenetic analysis of the TrpA enzyme family ............................................ 62 3.4.6 Cloning of tvTrpA2* and tvTrpB2a ................................................................... 63 3.4.7 Expression and purification of tvTrpA2* and tvTrpB2a .................................... 63 3.4.8 Activity of tvTrpA2* and tvTrpB2a .................................................................... 64 3.4.9 Probing the formation of a transient TS ........................................................... 65 3.4.10 Specificity of the subunit interaction within transient TS .................................. 67 3.4.11 Identification of a common interface within transient TS .................................. 68 3.4.12 Cloning of chimera TrpB2 proteins .................................................................. 69 3.4.13 Expression and purification of chimera TrpB2 proteins ................................... 70 3.4.14 Structural integrity, thermal stability, and activity of chimera TrpB2 proteins ... 71 3.4.15 Analysis of chimera TrpB2 proteins for their ability to form a transient TS ...... 73 3.5 Conclusion ................................................................................................................... 74 IMPLICATION FOR TS EVOLUTION....................................................................... 77 4 SUMMARY .......................................................................................................... 79 5 ZUSAMMENFASSUNG ...................................................................................... 82 6 MATERIALS ....................................................................................................... 85 6.1 Instrumentation ..........................................................................................................
Load more

Recommended publications
  • A Theoretical Study of the Tryptophan Synthase Enzyme Reaction Network
    A Theoretical Study of the Tryptophan Synthase Enzyme Reaction Network Dissertation zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) im Fach Chemie Spezialisierung: Physikalische und theoretische Chemie Eingereicht an der Mathematisch-Naturwissenschaftlichen Fakult¨at der Humboldt-Universit¨at zu Berlin von Dimitri Loutchko Pr¨asidentin der Humboldt-Universit¨atzu Berlin Prof. Dr.-Ing. Dr. Sabine Kunst Dekan der Mathematisch-Naturwissenschaftlichen Fakult¨at Prof. Dr. Elmar Kulke 1. Gutachter: Prof. Dr. Gerhard Ertl 2. Gutachter: Prof. Dr. Klaus Rademann 3. Gutachter: Prof. Dr. Yannick de Decker Tag der m¨undlichen Pr¨ufung:09.07.2018 ii Abstract iii Abstract The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine. It catalyzes the biosynthesis of tryptophan from serine and indole glycerol phos- phate. As a single macromolecule, it possesses two distinct catalytic subunits and implements 13 different elementary reaction steps. A complex pattern of allosteric regulation is involved in its operation. The catalytic activity in a subunit is enhanced or inhibited depending on the state of the other subunit. The gates controlling arrival and release of the ligands can become open or closed depending on the chemical states. The intermediate product indole is directly channeled within the protein from one subunit to another, so that it is never released into the solution around it. In this thesis, the first single-molecule kinetic model of the enzyme is proposed and analyzed. All its transition rate constants are extracted from available experimental data, and thus, no fitting parameters are employed. Numerical simulations reveal strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase.
    [Show full text]
  • Directed Evolution of the Tryptophan Synthase Β-Subunit for Stand-Alone Function Recapitulates Allosteric Activation
    Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation Andrew R. Buller1, Sabine Brinkmann-Chen1, David K. Romney, Michael Herger, Javier Murciano-Calles, and Frances H. Arnold2 Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 Edited by Alan R. Fersht, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom, and approved October 16, 2015 (received for review August 17, 2015) Enzymes in heteromeric, allosterically regulated complexes cata- associated with open, partially closed, and fully closed states lyze a rich array of chemical reactions. Separating the subunits of during the catalytic cycle (2, 4, 6). such complexes, however, often severely attenuates their catalytic TrpS is a naturally promiscuous enzyme complex: the model activities, because they can no longer be activated by their protein system from S. typhimurium catalyzes its β-substitution reaction partners. We used directed evolution to explore allosteric regula- with most haloindoles, methylindoles, and aminoindoles, along tion as a source of latent catalytic potential using the β-subunit of with an assortment of nonindole nucleophiles for C–S, C–N, and – tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of C C bond formation (7). Such noncanonical amino acids (NCAAs) its native αββα complex, TrpB efficiently produces tryptophan and have diverse applications in chemical biology (8), serve as inter- tryptophan analogs; activity drops considerably when it is used as mediates in the synthesis of natural products (9, 10), and are priv- a stand-alone catalyst without the α-subunit. Kinetic, spectro- ileged scaffolds for the development of pharmaceuticals (11).
    [Show full text]
  • Regional Compartmentalization in Multienzyme-Related Biomaterials System
    Regional Compartmentalization in Multienzyme-related Biomaterials System Zhexu Xi(1) Bristol Center of Functional Nanomaterials, School of Physics, University of Bristol(1) Abstract: Multienzyme cascaded reactions are widely utilized because they can generate value-added biomaterials and biodevices from simple raw materials. However, how to promote the catalytic efficiency and synergistic effect of the multienzyme system is proved to be a challengeable point. Recent discovery repeatedly emphasized the strategy of assembled multienzyme complexes or forming subcellular compartments for spacial optimization. This highly ordered and tunable organization contributes to various biochemical processes. This dissertation focuses mainly on analysis and progresses in this cascaded strategy, regarding the feasibility of regional compartments for natural or artificial biochemical reactions in vivo and vitro, simultaneously. Key words: compartments, spacial organization, enzyme assembly, bioreaction in vivo and in vitro 1. Introduction Recently, enzymes are increasingly used in cascaded reactions because of high selectivity to promote a biofriendly synthetic environment, like multienzyme cascaded reactions. Compared with traditional multistep sequential biosynthesis methods, enzyme cascades can relieve the bulk diffusion from unstable or toxic intermediates and avoid the intermediary product purification[1,2]. Additionally, sequential cascaded reactions in vivo are more attractive in the stage of the multienzyme assembled system. They can effectively eliminate product inhibition, improve cofactor regeneration and work without purification and immobilized enzymatic catalysts. Common methods of reaction pathways contain two following steps[1,3]. One is based on optimization and modification of natural intermediate metabolism by gene knockout or overexpression in the early period. Lonza et al.[4] found a biological process in natural metabolic pathways to synthesize L-carnitine from 4-butylamine.
    [Show full text]
  • Substrate Channeling in Proline Metabolism Benjamin W
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Biochemistry -- Faculty Publications Biochemistry, Department of 2012 Substrate channeling in proline metabolism Benjamin W. Arentson University of Nebraska-Lincoln, [email protected] Nikhilesh Sanyal University of Nebraska-Lincoln, [email protected] Donald F. Becker University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/biochemfacpub Part of the Biochemistry Commons, Biotechnology Commons, and the Other Biochemistry, Biophysics, and Structural Biology Commons Arentson, Benjamin W.; Sanyal, Nikhilesh; and Becker, Donald F., "Substrate channeling in proline metabolism" (2012). Biochemistry -- Faculty Publications. 303. http://digitalcommons.unl.edu/biochemfacpub/303 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Biochemistry -- Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. NIH Public Access Author Manuscript Front Biosci. Author manuscript; available in PMC 2013 January 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Front Biosci. ; 17: 375–388. Substrate channeling in proline metabolism Benjamin W. Arentson1, Nikhilesh Sanyal1, and Donald F. Becker1 1Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA Abstract Proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. Results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism.
    [Show full text]
  • Five Enzymes of the Arg/N-Degron Pathway Form a Targeting Complex: the Concept of Superchanneling
    Five enzymes of the Arg/N-degron pathway form a targeting complex: The concept of superchanneling Jang-Hyun Oha, Ju-Yeon Hyuna, Shun-Jia Chena, and Alexander Varshavskya,1 aDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 Contributed by Alexander Varshavsky, February 28, 2020 (sent for review February 18, 2020; reviewed by Thomas Arnesen and William P. Tansey) The Arg/N-degron pathway targets proteins for degradation by N-degron comprises, in particular, a destabilizing Nt-residue of recognizing their N-terminal (Nt) residues. If a substrate bears, a protein and its internal Lys residue(s) that acts as a site of for example, Nt-Asn, its targeting involves deamidation of Nt- polyubiquitylation (2, 21, 49). Asn, arginylation of resulting Nt-Asp, binding of resulting (conju- Eukaryotes contain the Arg/N-degron pathway (it recognizes, gated) Nt-Arg to the UBR1-RAD6 E3-E2 ubiquitin ligase, ligase- in particular, specific unacetylated Nt-residues) (Fig. 1), the Ac/ α mediated synthesis of a substrate-linked polyubiquitin chain, its N-degron pathway (it recognizes, in particular, the N -terminally capture by the proteasome, and substrate’s degradation. We dis- acetylated [Nt-acetylated] Nt-residues), the Pro/N-degron path- – covered that the human Nt-Asn specific Nt-amidase NTAN1, Nt- way (it recognizes, in particular, the Nt-Pro residue or a Pro at – Gln specific Nt-amidase NTAQ1, arginyltransferase ATE1, and the position 2), the Gly/N-degron pathway (it recognizes Nt-Gly), ubiquitin ligase UBR1-UBE2A/B (or UBR2-UBE2A/B) form a complex and the fMet/N-degron pathway (it recognizes proteins that had in which NTAN1 Nt-amidase binds to NTAQ1, ATE1, and UBR1/ been “pretranslationally” Nt-formylated) (SI Appendix, Fig.
    [Show full text]
  • Substrate Channeling and Enzyme Complexes for Biotechnological Applications
    Biotechnology Advances 29 (2011) 715–725 Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv Research review paper Substrate channeling and enzyme complexes for biotechnological applications Y.-H. Percival Zhang ⁎ Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Tech, Blacksburg, VA 24061, USA Institute for Critical Technology and Applied Science, Virginia Tech, Blacksburg, VA 24061, USA DOE Bioenergy Science Center, Oak Ridge, TN 37831, USA Gate Fuels Inc. 3107 Alice Drive, Blacksburg, VA 24060, USA article info abstract Article history: Substrate channeling is a process of transferring the product of one enzyme to an adjacent cascade enzyme or Received 11 November 2010 cell without complete mixing with the bulk phase. Such phenomena can occur in vivo, in vitro, or ex vivo. Received in revised form 19 May 2011 Enzyme–enzyme or enzyme–cell complexes may be static or transient. In addition to enhanced reaction rates Accepted 30 May 2011 through substrate channeling in complexes, numerous potential benefits of such complexes are protection of Available online 7 June 2011 unstable substrates, circumvention of unfavorable equilibrium and kinetics imposed, forestallment of substrate competition among different pathways, regulation of metabolic fluxes, mitigation of toxic Keywords: Cell-free synthetic pathway metabolite inhibition, and so on. Here we review numerous examples of natural and synthetic complexes biotransformation featuring substrate channeling. Constructing synthetic in vivo, in vitro or ex vivo complexes for substrate Coimmobilization channeling would have great biotechnological potentials in metabolic engineering, multi-enzyme-mediated Enzyme complex biocatalysis, and cell-free synthetic pathway biotransformation (SyPaB). Metabolic engineering © 2011 Elsevier Inc.
    [Show full text]
  • Modeling and Computational Prediction of Metabolic Channelling
    MODELING AND COMPUTATIONAL PREDICTION OF METABOLIC CHANNELLING by Christopher Morran Sanford A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Christopher Morran Sanford 2009 Abstract MODELING AND COMPUTATIONAL PREDICTION OF METABOLIC CHANNELLING Master of Science 2009 Christopher Morran Sanford Graduate Department of Molecular Genetics University of Toronto Metabolic channelling occurs when two enzymes that act on a common substrate pass that intermediate directly from one active site to the next without allowing it to diffuse into the surrounding aqueous medium. In this study, properties of channelling are investigated through the use of computational models and cell simulation tools. The effects of enzyme kinetics and thermodynamics on channelling are explored with the emphasis on validating the hypothesized roles of metabolic channelling in living cells. These simulations identify situations in which channelling can induce acceleration of reaction velocities and reduction in the free concentration of intermediate metabolites. Databases of biological information, including metabolic, thermodynamic, toxicity, inhibitory, gene fusion and physical protein interaction data are used to predict examples of potentially channelled enzyme pairs. The predictions are used both to support the hypothesized evolutionary motivations for channelling, and to propose potential enzyme interactions that may be worthy of future investigation. ii Acknowledgements I wish to thank my supervisor Dr. John Parkinson for the guidance he has provided during my time spent in his lab, as well as for his extensive help in the writing of this thesis. I am grateful for the advice of my committee members, Prof.
    [Show full text]
  • Plastid-Localized Amino Acid Biosynthetic Pathways of Plantae Are Predominantly Composed of Non-Cyanobacterial Enzymes
    Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly SUBJECT AREAS: MOLECULAR EVOLUTION composed of non-cyanobacterial PHYLOGENETICS PLANT EVOLUTION enzymes PHYLOGENY Adrian Reyes-Prieto1* & Ahmed Moustafa2* Received 1 26 September 2012 Canadian Institute for Advanced Research and Department of Biology, University of New Brunswick, Fredericton, Canada, 2Department of Biology and Biotechnology Graduate Program, American University in Cairo, Egypt. Accepted 27 November 2012 Studies of photosynthetic eukaryotes have revealed that the evolution of plastids from cyanobacteria Published involved the recruitment of non-cyanobacterial proteins. Our phylogenetic survey of .100 Arabidopsis 11 December 2012 nuclear-encoded plastid enzymes involved in amino acid biosynthesis identified only 21 unambiguous cyanobacterial-derived proteins. Some of the several non-cyanobacterial plastid enzymes have a shared phylogenetic origin in the three Plantae lineages. We hypothesize that during the evolution of plastids some enzymes encoded in the host nuclear genome were mistargeted into the plastid. Then, the activity of those Correspondence and foreign enzymes was sustained by both the plastid metabolites and interactions with the native requests for materials cyanobacterial enzymes. Some of the novel enzymatic activities were favored by selective compartmentation should be addressed to of additional complementary enzymes. The mosaic phylogenetic composition of the plastid amino acid A.R.-P. ([email protected]) biosynthetic pathways and the reduced number of plastid-encoded proteins of non-cyanobacterial origin suggest that enzyme recruitment underlies the recompartmentation of metabolic routes during the evolution of plastids. * Equal contribution made by these authors. rimary plastids of plants and algae are the evolutionary outcome of an endosymbiotic association between eukaryotes and cyanobacteria1.
    [Show full text]
  • An Investigation of the Molecular Determinants of Substrate Channeling and Allosteric Activation in Aldolase-Dehydrogenase Complexes
    An Investigation of the Molecular Determinants of Substrate Channeling and Allosteric Activation in Aldolase-Dehydrogenase Complexes By Jason Carere A Thesis presented to The University of Guelph In partial fulfillment of requirements for the degree of Doctor of Philosophy in Molecular and Cellular Biology Guelph, Ontario, Canada © Jason Carere, April, 2013 Abstract An Investigation of the Molecular Determinants of Substrate Channeling and Allosteric Activation in Aldolase-Dehydrogenase Complexes Jason Carere Advisor: University of Guelph 2013 Stephen Seah The aldolase-dehydrogenase complex catalyzes the last two steps in the microbial meta- cleavage pathway of various aromatic compounds including polychlorinated biphenyls (bph pathway) and cholesterol (hsa pathway). The aldolase, BphI, cleaves 4-hydroxy-2-oxoacids to produce pyruvate and an aldehyde. Linear aldehydes of up to six carbons long and branched isobutyraldehyde were directly channeled to the aldehyde dehydrogenase BphJ, via a molecular tunnel, with greater than 80% efficiency. The molecular tunnel is narrow in positions lined by Gly-322 and Gly-323 in the aldolase. BphI variants G322F, G322L and G323F were found to block aldehyde channeling. The replacement of Asn-170 in BphJ with alanine and aspartate did not substantially alter aldehyde channeling efficiencies, thus disproving a previous hypothesis that hydrogen bonding between the Asn-170 and the nicotinamide cofactor induces the opening of the exit of the tunnel. The H20A and Y290F BphI variants displayed significantly reduced aldehyde channeling efficiencies indicating that these residues control the entry and exit of substrates and products from the aldolase reaction. The BphI reaction was activated by NADH binding to BphJ in the wild-type enzyme and channel blocked variants.
    [Show full text]
  • Carbamoyl Phosphate Synthetase: a Tunnel Runs Through It Hazel M Holden*, James B Thodent and Frank M Raushel
    679 Carbamoyl phosphate synthetase: a tunnel runs through it Hazel M Holden*, James B Thodent and Frank M Raushel The direct transfer of metabolites from one protein to another Biochemistry of carbamoyl phosphate in a biochemical pathway or between one active site and synthetase another within a single enzyme has been described as Carbamoyl phosphate synthetase, hereafter referred to as substrate channeling. The first structural visualization of such a CPS, plays a critical role in both arginine and pyrimidine phenomenon was provided by the X-ray crystallographic biosynthesis by providing an essential precursor, namely analysis of tryptophan synthase, in which a tunnel of carbamoyl phosphate. This remarkable enzyme has been approximately 25/~, in length was observed. The recently the focus of intense investigation for more than 30 years, determined three-dimensional structure of carbamoyl due, in part, to both its important metabolic role and the phosphate synthetase sets a new long distance record in that large number of substrates, products and effector mole- the three active sites are separated by nearly 1 O0 A. cules that bind to it. Addresses According to most biochemical data, CPS catalyzes the *tDepartment of Biochemistry, University of Wisconsin, Madison, production of carbamoyl phosphate from one molecule of W153706, USA bicarbonate, two molecules of MgZ+ATP and one molecule *e-mail: holden @enzyrne,wisc.edu re-mail: [email protected] of glutamine, as depicted in Scheme I below [3,4]. $Department of Chemistry, and Department
    [Show full text]
  • Can Enzyme Proximity Accelerate Cascade Reactions? Andrij Kuzmak 1, Sheiliza Carmali 2,3, Eric Von Lieres 4, Alan J
    www.nature.com/scientificreports OPEN Can enzyme proximity accelerate cascade reactions? Andrij Kuzmak 1, Sheiliza Carmali 2,3, Eric von Lieres 4, Alan J. Russell 3,5 & Svyatoslav Kondrat 4,6 Received: 1 August 2018 The last decade has seen an exponential expansion of interest in conjugating multiple enzymes of Accepted: 26 November 2018 cascades in close proximity to each other, with the overarching goal being to accelerate the overall Published: xx xx xxxx reaction rate. However, some evidence has emerged that there is no efect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a signifcant enhancement can only be achieved for difusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the efect of channeling quantitatively and demonstrate that proximity can have a more pronounced efect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions. Enzyme-catalyzed reactions are probably the most ubiquitous and elegant reactions on Earth. Typically an enzyme-catalyzed reaction does not occur alone, but instead is a part of a natural metabolic pathway or synthetic cascade. A particular role in enzymatic cascades is played by metabolite or substrate channeling, in which the product of one reaction is directly passed to the active site of the next enzyme in a cascade, either via a physical tunnel in an enzyme-enzyme complex1–4, along an ‘electrostatic highway’3–6, or through proximity of two (or more) enzymes7–10.
    [Show full text]
  • Life with Carbon Monoxide
    Critical Reviews in Biochemistry and Molecular Biology, 39:165–195, 2004 Copyright c Taylor & Francis Inc. ISSN: 1040-9238 print / 1549-7798 online DOI: 10.1080/10409230490496577 Life with Carbon Monoxide Stephen W. Ragsdale Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln, NE, USA CO by generating carbon monoxide as a metabolic inter- This review focuses on how microbes live on CO as a sole source mediate. Since CO is an inorganic carbon source, we will of carbon and energy and with CO by generating carbon monox- consider growth on CO as autotrophic, although Wilhelm ide as a metabolic intermediate. The use of CO is a property of Pfeffer’s 1897 definition, which is still used today, includes organisms that use the Wood-L jungdahl pathway of autotrophic organisms able to synthesize their cell substance from in- growth. The review discusses when CO metabolism originated, organic carbonate as their main source of carbon (Brock when and how it was discovered, and what properties of CO are & Schlegel, 1989). The use of CO, a toxic gas to animals, ideal for microbial growth. How CO sensing by a heme-containing as a metabolic building block is an interesting property transcriptional regulatory protein activates the expression of CO of certain classes of diverse organisms that can grow on metabolism-linked genes is described. Two metalloenzymes are the CO2 by any of the known CO2 fixation pathways as long cornerstones of growth with CO: CO dehydrogenase (CODH) and as they have a mechanism for converting CO into CO . acetyl-CoA synthase (ACS). CODH oxidizes CO to CO ,providing 2 2 This review will focus on the enzyme, CO dehydrogenase low-potential electrons for the cell, or alternatively reduces CO2 to CO.
    [Show full text]