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Thioester synthesis by a designed nickel enzyme models prebiotic energy conversion. Proc Natl Acad Sci U S A 2022; 119:e2123022119. [PMID: 35858422 PMCID: PMC9335327 DOI: 10.1073/pnas.2123022119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The formation of carbon-carbon bonds from prebiotic precursors such as carbon dioxide represents the foundation of all primordial life processes. In extant organisms, this reaction is carried out by the carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS) enzyme, which performs the cornerstone reaction in the ancient Wood-Ljungdahl metabolic pathway to synthesize the key biological metabolite, acetyl-CoA. Despite its significance, a fundamental understanding of this transformation is lacking, hampering efforts to harness analogous chemistry. To address these knowledge gaps, we have designed an artificial metalloenzyme within the azurin protein scaffold as a structural, functional, and mechanistic model of ACS. We demonstrate the intermediacy of the NiI species and requirement for ordered substrate binding in the bioorganometallic carbon-carbon bond-forming reaction from the one-carbon ACS substrates. The electronic and geometric structures of the nickel-acetyl intermediate have been characterized using time-resolved optical, electron paramagnetic resonance, and X-ray absorption spectroscopy in conjunction with quantum chemical calculations. Moreover, we demonstrate that the nickel-acetyl species is chemically competent for selective acyl transfer upon thiol addition to biosynthesize an activated thioester. Drawing an analogy to the native enzyme, a mechanism for thioester generation by this ACS model has been proposed. The fundamental insight into the enzymatic process provided by this rudimentary ACS model has implications for the evolution of primitive ACS-like proteins. Ultimately, these findings offer strategies for development of highly active catalysts for sustainable generation of liquid fuels from one-carbon substrates, with potential for broad applications across diverse fields ranging from energy storage to environmental remediation.
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Abstract
The biological synthesis of acetyl-coenzyme A (acetyl-CoA), catalyzed by acetyl-CoA synthase (ACS), is of biological significance and chemical interest acting as a source of energy and carbon. The catalyst contains an unusual hexa-metal cluster with two nickel ions and a [Fe4S4] cluster. DFT calculations have been performed to investigate the ACS reaction mechanism starting from three different oxidation states (+2, +1, and 0) of Nip, the nickel proximal to [Fe4S4]. The results indicate that the ACS reaction proceeds first through a methyl radical transfer from cobalamin (Cbl) to Nip randomly accompanying with the CO binding. After that, C-C bond formation occurs between the Nip-bound methyl and CO, forming Nip-acetyl. The substrate CoA-S- then binds to Nip, allowing C-S bond formation between the Nip-bound acetyl and CoA-S-. Methyl transfer is rate-limiting with a barrier of ∼14 kcal/mol, which does not depend on the presence or absence of CO. Both the Nip2+ and Nip1+ states are chemically capable of catalyzing the ACS reaction independent of the state (+2 or +1) of the [Fe4S4] cluster. The [Fe4S4] cluster is not found to affect the steps of methyl transfer and C-C bond formation but may be involved in the C-S bond formation depending on the detailed mechanism chosen. An ACS active site containing a Nip(0) state could not be obtained. Optimizations always led to a Nip1+ state coupled with [Fe4S4]1+. The calculations show a comparable activity for Nip1+/[Fe4S4]1+, Nip1+/[Fe4S4]2+, and Nip2+/[Fe4S4]2+. The results here give significant insights into the chemistry of the important ACS reaction.
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Affiliation(s)
- Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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3
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Burton R, Can M, Esckilsen D, Wiley S, Ragsdale SW. Production and properties of enzymes that activate and produce carbon monoxide. Methods Enzymol 2018; 613:297-324. [PMID: 30509471 PMCID: PMC6309614 DOI: 10.1016/bs.mie.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The chapter focuses on the methods involved in producing and characterizing two key nickel-iron-sulfur enzymes in the Wood-Ljungdahl pathway (WLP) of anaerobic conversion of carbon dioxide fixation into acetyl-CoA: carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS). The WLP is used for biosynthesis of cell material and energy conservation by anaerobic bacteria and archaea, and it is central to several industrial biotechnology processes aimed at using syngas and waste gases for the production of fuels and chemicals. The pathway can run in reverse to allow organisms, e. g., methanogens and sulfate reducers, to grow on acetate. The CODH and ACS intertwine to form a tenacious CODH/ACS complex that converts CO2, a methyl group, and coenzyme A into acetyl-CoA. CODH also behaves as a modular unit that can function as an independent homodimer. Besides coupling to ACS, CODH can interact with hydrogenases to couple CO oxidation to H2 formation. These enzymes have been purified and characterized from several microbes.
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Affiliation(s)
- Rodney Burton
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Daniel Esckilsen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Seth Wiley
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, United States.
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Can M, Armstrong F, Ragsdale SW. Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase. Chem Rev 2014; 114:4149-74. [PMID: 24521136 PMCID: PMC4002135 DOI: 10.1021/cr400461p] [Citation(s) in RCA: 373] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Mehmet Can
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fraser
A. Armstrong
- Inorganic
Chemistry Laboratory, University of Oxford Oxford, OX1 3QR, United Kingdom
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Grahame DA. Methods for analysis of acetyl-CoA synthase applications to bacterial and archaeal systems. Methods Enzymol 2011; 494:189-217. [PMID: 21402216 DOI: 10.1016/b978-0-12-385112-3.00010-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nickel- and iron-containing enzyme acetyl-CoA synthase (ACS) catalyzes de novo synthesis as well as overall cleavage of acetyl-CoA in acetogens, various other anaerobic bacteria, methanogens, and other archaea. The enzyme contains a unique active site metal cluster, designated the A cluster, that consists of a binuclear Ni-Ni center bridged to an [Fe(4)S(4)] cluster. In bacteria, ACS is tightly associated with CO dehydrogenase to form the bifunctional heterotetrameric enzyme CODH/ACS, whereas in archaea, ACS is a component of the large multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS), which comprises five different subunits that make up the subcomponent proteins ACS, CODH, and a corrinoid enzyme. Characteristic properties of ACS are discussed, and key methods are described for analysis of the enzyme's multiple redox-dependent activities, including overall acetyl-CoA synthesis, acetyltransferase, and an isotopic exchange reaction between the carbonyl group of acetyl-CoA and CO. Systematic measurement of these activities, applied to different ACS protein forms, provides insight into the ACS catalytic mechanism and physiological functions in both CODH/ACS and ACDS systems.
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Affiliation(s)
- David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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Ragsdale SW, Pierce E. Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:1873-98. [PMID: 18801467 PMCID: PMC2646786 DOI: 10.1016/j.bbapap.2008.08.012] [Citation(s) in RCA: 714] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/12/2008] [Accepted: 08/13/2008] [Indexed: 01/04/2023]
Abstract
Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.
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Affiliation(s)
- Stephen W Ragsdale
- Department of Biological Chemistry, MSRB III, 5301, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109-0606, USA.
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7
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Seravalli J, Ragsdale SW. Pulse-chase studies of the synthesis of acetyl-CoA by carbon monoxide dehydrogenase/acetyl-CoA synthase: evidence for a random mechanism of methyl and carbonyl addition. J Biol Chem 2008; 283:8384-94. [PMID: 18203715 DOI: 10.1074/jbc.m709470200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbon monoxide dehydrogenase/acetyl-CoA synthase catalyzes acetyl-CoA synthesis from CO, CoA, and a methylated corrinoid iron-sulfur protein, which acts as a methyl donor. This reaction is the last step in the Wood-Ljungdahl pathway of anaerobic carbon fixation. The binding sequence for the three substrates has been debated for over a decade. Different binding orders imply different mechanisms (i.e. paramagnetic versus diamagnetic mechanisms). Ambiguity arises because CO and CoA can each undergo isotopic exchange with acetyl-CoA, suggesting that either of these two substrates could be the last to bind to the acetyl-CoA synthase active site. Furthermore, carbonylation, CoA binding, and methyl transfer can all occur in the absence of the other two substrates. Here, we report pulse-chase studies, which unambiguously establish the order in which the three substrates bind. Although a CoA pulse is substantially diluted by excess CoA in the chase, isotope recovery of a pulse of labeled CO or methyl group is unaffected by the presence of excess unlabeled CO or methyl group in the chase. These results demonstrate that CoA is the last substrate to bind and that CO and the methyl group bind randomly as the first substrate in acetyl-CoA synthesis. Up to 100% of the methyl groups and CoA and up to 60-70% of the CO employed in the pulse phase can be trapped in the product acetyl-CoA.
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Affiliation(s)
- Javier Seravalli
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588-0664, USA
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9
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Maynard EL, Sewell C, Lindahl PA. Kinetic mechanism of acetyl-CoA synthase: steady-state synthesis at variable Co/Co2 pressures. J Am Chem Soc 2001; 123:4697-703. [PMID: 11457278 DOI: 10.1021/ja004017t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Steady-state initial rates of acetyl-CoA synthesis (upsilon/[E(tot)]) catalyzed by acetyl-CoA synthase from Clostridium thermoaceticum (ACS) were determined at various partial pressures of CO and CO2. When [CO] was varied from 0 to 100 microM in a balance of Ar, rates increased sharply from 0.3 to 100 min(-1). At [CO] > 100 microM, rates declined sharply and eventually stabilized at 10 min(-1) at 980 microM CO. Equivalent experiments carried out in CO2 revealed similar inhibitory behavior and residual activity under saturating [CO]. Plots of upsilon/[E(tot)] vs [CO2] at different fixed inhibitory [CO] revealed that Vmax/[E(tot)] (kcat) decreased with increasing [CO]. Plots of upsilon/[E(tot)] vs [CO2] at different fixed noninhibitory [CO] showed that Vmax/[E(tot)] was insensitive to changes in [CO]. Of eleven candidate mechanisms, the simplest one that fit the data best had the following key features: (a) either CO or CO2 (at a designated reductant level and pH) activate the enzyme (E' + CO right arrow over left arrow E, E' + CO2/2e-/2H+ right arrow over left arrow E); (b) CO and CO2 are both substrates that compete for the same enzyme form (E + CO right arrow over left arrow ECO, E + CO2/2e-/2H+ right arrow over left arrow ECO, and ECO --> E + P); (c) between 3 and 5 molecules of CO bind cooperatively to an enzyme form different from that to which CO2 and substrate CO bind (nCO + ECO right arrow over left arrow (CO)nECO), and this inhibits catalysis; and (d) the residual activity arises from either the (CO)nECO state or a heterogeneous form of the enzyme. Implications of these results, focusing on the roles of CO and CO2 in catalysis, are discussed.
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Affiliation(s)
- E L Maynard
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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Mishra PK, Drueckhammer DG. Coenzyme A Analogues and Derivatives: Synthesis and Applications as Mechanistic Probes of Coenzyme A Ester-Utilizing Enzymes. Chem Rev 2000; 100:3283-3310. [PMID: 11777425 DOI: 10.1021/cr990010m] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pranab K. Mishra
- Department of Chemistry, State University at Stony Brook, Stony Brook, New York 11794
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11
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DeRose VJ, Telser J, Anderson ME, Lindahl PA, Hoffman BM. A Multinuclear ENDOR Study of the C-Cluster in CO Dehydrogenase from Clostridium thermoaceticum: Evidence for HxO and Histidine Coordination to the [Fe4S4] Center. J Am Chem Soc 1998. [DOI: 10.1021/ja9731480] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victoria J. DeRose
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Joshua Telser
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Mark E. Anderson
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Paul A. Lindahl
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Brian M. Hoffman
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
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12
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Russell WK, Stålhandske CMV, Xia J, Scott RA, Lindahl PA. Spectroscopic, Redox, and Structural Characterization of the Ni-Labile and Nonlabile Forms of the Acetyl-CoA Synthase Active Site of Carbon Monoxide Dehydrogenase. J Am Chem Soc 1998. [DOI: 10.1021/ja981165z] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- William K. Russell
- Contribution from the Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Center for Metalloenzyme Studies and Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Christina M. V. Stålhandske
- Contribution from the Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Center for Metalloenzyme Studies and Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Jinqiang Xia
- Contribution from the Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Center for Metalloenzyme Studies and Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Robert A. Scott
- Contribution from the Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Center for Metalloenzyme Studies and Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Paul A. Lindahl
- Contribution from the Department of Chemistry, Texas A&M University, College Station, Texas 77843, and Center for Metalloenzyme Studies and Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
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13
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Xia J, Hu Z, Popescu CV, Lindahl PA, Münck E. Mössbauer and EPR Study of the Ni-Activated α-Subunit of Carbon Monoxide Dehydrogenase fromClostridium thermoaceticum. J Am Chem Soc 1997. [DOI: 10.1021/ja971025+] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Barondeau DP, Lindahl PA. Methylation of Carbon Monoxide Dehydrogenase fromClostridium thermoaceticumand Mechanism of Acetyl Coenzyme A Synthesis. J Am Chem Soc 1997. [DOI: 10.1021/ja963597k] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Ragsdale SW, Kumar M. Nickel-Containing Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase(,). Chem Rev 1996; 96:2515-2540. [PMID: 11848835 DOI: 10.1021/cr950058+] [Citation(s) in RCA: 224] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen W. Ragsdale
- Department of Biochemistry, Beadle Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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16
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Hu Z, Spangler NJ, Anderson ME, Xia J, Ludden PW, Lindahl PA, Münck E. Nature of the C-Cluster in Ni-Containing Carbon Monoxide Dehydrogenases. J Am Chem Soc 1996. [DOI: 10.1021/ja9528386] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhengguo Hu
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Nathan J. Spangler
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Mark E. Anderson
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Jinqiang Xia
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Paul W. Ludden
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Paul A. Lindahl
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
| | - Eckard Münck
- Contribution from the Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, Department of Chemistry, Texas A & M University, College Station, Texas 77843, and Department of Biochemistry, College of Agricultural and Life Sciences, University of WisconsinMadison, Madison, Wisconsin 53706
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Affiliation(s)
- F C Wedler
- Department of Molecular and Cell Biology, Althause Laboratory, Pennsylvania State University, University Park 16802, USA
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Shin W, Lindahl PA. Low spin quantitation of NiFeC EPR signal from carbon monoxide dehydrogenase is not due to damage incurred during protein purification. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1161:317-22. [PMID: 8381672 DOI: 10.1016/0167-4838(93)90231-f] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Evidence is presented that the O2-sensitive, nickel- and iron-containing enzyme carbon monoxide dehydrogenase from Clostridium thermoaceticum was purified without significantly inactivating either its CO oxidation or CO/acetyl-CoA exchange activities. All CO oxidation activity from the crude extract was recovered in the purified enzyme (and side fractions). The exchange activity could not be quantified similarly, because the crude extract and early purification step fractions exhibited little or no exchange activity. Later purification fractions exhibited much more exchange activity, suggesting that an inhibitor was present in the impure fractions. The NiFeC EPR signal intensity was used as an indicator of the enzyme's capacity to catalyze exchange. This signal was extremely sensitive to oxygen; exposure to as little as 0.5 equiv/mol enzyme dimer resulted in substantial loss of intensity. The NiFeC intensities at each step in the purification were virtually invariant, indicating that the enzyme had not been exposed to oxygen and had not been inactivated towards catalyzing exchange. The ability to purify carbon monoxide dehydrogenase (CODH) without inactivating nearly any of the molecules suggests that it is quite stable under anaerobic conditions. The purified enzyme, which could not have lost functional metal ions during purification, contained 1.9 Ni and 11.3 Fe, similar to previous reports. The NiFeC EPR signal intensity from each purification fraction (0.2 spins/mol enzyme dimer) was as low as from previous preparations, indicating that its low spin quantitation is not the result of damage incurred during purification. If the low intensity arises from heterogeneity as proposed earlier, the heterogeneity must originate prior to purification.
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Affiliation(s)
- W Shin
- Department of Chemistry, Texas A&M University, College Station 77843
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Shin W, Lindahl PA. Function and CO binding properties of the NiFe complex in carbon monoxide dehydrogenase from Clostridium thermoaceticum. Biochemistry 1992; 31:12870-5. [PMID: 1334436 DOI: 10.1021/bi00166a023] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adding 1,10-phenanthroline to carbon monoxide dehydrogenase from Clostridium thermoaceticum results in the complete loss of the NiFeC EPR signal and the CO/acetyl-CoA exchange activity. Other EPR signals characteristic of the enzyme (the gav = 1.94 and gav = 1.86 signals) and the CO oxidation activity are completely unaffected by the 1,10-phenanthroline treatment. This indicates that there are two catalytic sites on the enzyme; the NiFe complex is required for catalyzing the exchange and acetyl-CoA synthase reactions, while some other site is responsible for CO oxidation. The strength of CO binding to the NiFe complex was examined by titrating dithionite-reduced enzyme with CO. During the titration, the NiFeC EPR signal developed to a final spin intensity of 0.23 spin/alpha beta. The resulting CO titration curve (NiFeC spins/alpha beta vs CO pha beta) was fitted using two reactions: binding of CO to the oxidized NiFe complex, and reduction of the CO-bound species to a form that exhibits the NiFeC signal. Best fits yielded apparent binding constants between 6000 and 14,000 M-1 (Kd = 70-165 microM). This sizable range is due to uncertainty whether CO binds to all or only a small fraction (approximately 23%) of the NiFe complexes. Reduction of the CO-bound NiFe complex is apparently required to activate it for catalysis. The electron used for this reduction originates from the CO oxidation site, suggesting that delivery of a low-potential electron to the CO-bound NiFe complex is the physiological function of the CO oxidation reaction catalyzed by this enzyme.
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Affiliation(s)
- W Shin
- Department of Chemistry, Texas A&M University, College Station 77843
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20
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Roberts JR, Lu WP, Ragsdale SW. Acetyl-coenzyme A synthesis from methyltetrahydrofolate, CO, and coenzyme A by enzymes purified from Clostridium thermoaceticum: attainment of in vivo rates and identification of rate-limiting steps. J Bacteriol 1992; 174:4667-76. [PMID: 1624454 PMCID: PMC206262 DOI: 10.1128/jb.174.14.4667-4676.1992] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many anaerobic bacteria fix CO2 via the acetyl-coenzyme A (CoA) (Wood) pathway. Carbon monoxide dehydrogenase (CODH), a corrinoid/iron-sulfur protein (C/Fe-SP), methyltransferase (MeTr), and an electron transfer protein such as ferredoxin II play pivotal roles in the conversion of methyltetrahydrofolate (CH3-H4folate), CO, and CoA to acetyl-CoA. In the study reported here, our goals were (i) to optimize the method for determining the activity of the synthesis of acetyl-CoA, (ii) to evaluate how closely the rate of synthesis of acetyl-CoA by purified enzymes approaches the rate at which whole cells synthesize acetate, and (iii) to determine which steps limit the rate of acetyl-CoA synthesis. In this study, CODH, MeTr, C/Fe-SP, and ferredoxin were purified from Clostridium thermoaceticum to apparent homogeneity. We optimized conditions for studying the synthesis of acetyl-CoA and found that when the reaction is dependent upon MeTr, the rate is 5.3 mumol min-1 mg-1 of MeTr. This rate is approximately 10-fold higher than that reported previously and is as fast as that predicted on the basis of the rate of in vivo acetate synthesis. When the reaction is dependent upon CODH, the rate of acetyl-CoA synthesis is approximately 0.82 mumol min-1 mg-1, approximately 10-fold higher than that observed previously; however, it is still lower than the rate of in vivo acetate synthesis. It appears that at least two steps in the overall synthesis of acetyl-CoA from CH3-H4folate, CO, and CoA can be partially rate limiting. At optimal conditions of low pH (approximately 5.8) and low ionic strength, the rate-limiting step involves methylation of CODH by the methylated C/Fe-SP. At higher pH values and/or higher ionic strength, transfer of the methyl group of CH3-H4folate to the C/Fe-SP becomes rate limiting.
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Affiliation(s)
- J R Roberts
- Department of Chemistry, University of Wisconsin, Milwaukee 53201
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21
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Morton T, Runquist J, Ragsdale S, Shanmugasundaram T, Wood H, Ljungdahl L. The primary structure of the subunits of carbon monoxide dehydrogenase/acetyl-CoA synthase from Clostridium thermoaceticum. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54357-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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22
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Gorst C, Ragsdale S. Characterization of the NiFeCO complex of carbon monoxide dehydrogenase as a catalytically competent intermediate in the pathway of acetyl-coenzyme A synthesis. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54763-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Reductive activation of the coenzyme A/acetyl-CoA isotopic exchange reaction catalyzed by carbon monoxide dehydrogenase from Clostridium thermoaceticum and its inhibition by nitrous oxide and carbon monoxide. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(19)67831-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Jetten MS, Hagen WR, Pierik AJ, Stams AJ, Zehnder AJ. Paramagnetic centers and acetyl-coenzyme A/CO exchange activity of carbon monoxide dehydrogenase from Methanothrix soehngenii. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 195:385-91. [PMID: 1847679 DOI: 10.1111/j.1432-1033.1991.tb15717.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Carbon monoxide (CO) dehydrogenase was purified, both aerobically and anaerobically, to apparent homogeneity from Methanothrix soehngenii. The enzyme contained 18 +/- 2 (n = 6) mol Fe/mol and 2.0 +/- 0.1 (n = 6) mol Ni/mol. Electron paramagnetic resonance (EPR) spectra of the aerobically purified CO dehydrogenase showed one sharp EPR signal at g = 2.014 with several characteristics of a [3Fe-4S]1+ cluster. The integrated intensity of this signal was low, 0.03 S = 1/2 spin/alpha beta dimer. The 3Fe spectrum was not affected by incubation with CO or acetyl-coenzyme A, but could be reduced by dithionite. The spectrum of the reduced, aerobically purified enzyme showed complex EPR spectra, which had several properties typical of two [4Fe-4S]1+ clusters, whose S = 1/2 spins weakly interacted by dipolar coupling. The integrated intensity was 0.1-0.2 spin/alpha beta dimer. The anaerobically isolated enzyme showed EPR spectra different from the reduced aerobically purified enzyme. Two major signals were apparent. One with g values of 2.05, 1.93 and 1.865, and an Em7.5 of -410 mV, which quantified to 0.9 S = 1/2 spin/alpha beta dimer. The other signal with g values of 1.997, 1.886 and 1.725, and an Em7.5 of -230 mV gave 0.1 spin/alpha beta dimer. When the enzyme was incubated with its physiological substrate acetyl-coenzyme A, these two major signals disappeared. Incubation of the enzyme under CO atmosphere resulted in a partial disappearance of the spectral component with g = 1.997, 1.886, 1.725. Acetyl-coenzyme A/CO exchange activity, 35 nmol.min-1.mg-1 protein, which corresponded to 7 mol CO exchanged min-1 mol-1 enzyme, could be detected in anaerobic enzyme preparations, but was absent in aerobic preparations. Carbon dioxide also exchanged with C-1 of acetyl-coenzyme A, but at a much lower rate than CO and to a much lower extent.
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Affiliation(s)
- M S Jetten
- Department of Microbiology, Wageningen Agricultural University, The Netherlands
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25
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Demonstration of carbon-carbon bond cleavage of acetyl coenzyme A by using isotopic exchange catalyzed by the CO dehydrogenase complex from acetate-grown Methanosarcina thermophila. J Bacteriol 1991; 173:929-32. [PMID: 1987173 PMCID: PMC207094 DOI: 10.1128/jb.173.2.929-932.1991] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The purified nickel-containing CO dehydrogenase complex isolated from methanogenic Methanosarcina thermophila grown on acetate is able to catalyze the exchange of [1-14C] acetyl-coenzyme A (CoA) (carbonyl group) with 12CO as well as the exchange of [3'-32P]CoA with acetyl-CoA. Kinetic parameters for the carbonyl exchange have been determined: Km (acetyl-CoA) = 200 microM, Vmax = 15 min-1. CoA is a potent inhibitor of this exchange (Ki = 25 microM) and is formed under the assay conditions because of a slow but detectable acetyl-CoA hydrolase activity of the enzyme. Kinetic parameters for both exchanges are compared with those previously determined for the acetyl-CoA synthase/CO dehydrogenase from the acetogenic Clostridium thermoaceticum. Collectively, these results provide evidence for the postulated role of CO dehydrogenase as the key enzyme for acetyl-CoA degradation in acetotrophic bacteria.
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Abstract
We know of three routes that organisms have evolved to synthesize complex organic molecules from CO2: the Calvin cycle, the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway. This review describes the enzymatic steps involved in the acetyl-CoA pathway, also called the Wood pathway, which is the major mechanism of CO2 fixation under anaerobic conditions. The acetyl-CoA pathway is also able to form acetyl-CoA from carbon monoxide. There are two parts to the acetyl-CoA pathway: (1) reduction of CO2 to methyltetrahydrofolate (methyl-H4folate) and (2) synthesis of acetyl-CoA from methyl-H4folate, a carboxyl donor such as CO or CO2, and CoA. This pathway is unique in that the major intermediates are enzyme-bound and are often organometallic complexes. Our current understanding of the pathway is based on radioactive and stable isotope tracer studies, purification of the component enzymes (some extremely oxygen sensitive), and identification of the enzyme-bound intermediates by chromatographic, spectroscopic, and electrochemical techniques. This review describes the remarkable series of enzymatic steps involved in acetyl-CoA formation by this pathway that is a key component of the global carbon cycle.
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Affiliation(s)
- S W Ragsdale
- Department of Chemistry, University of Wisconsin-Milwaukee
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Ragsdale SW, Baur J, Gorst C, Harder S, Lu WP, Roberts D, Runquist J, Schiau I. The acetyl-CoA synthase fromClostridium thermoaceticum: from gene cluster to achive-site metal clusters. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04943.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Lindahl PA, Ragsdale SW, Münck E. Mössbauer study of CO dehydrogenase from Clostridium thermoaceticum. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39676-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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30
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CO dehydrogenase from Clostridium thermoaceticum. EPR and electrochemical studies in CO2 and argon atmospheres. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39675-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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31
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Lu WP, Harder SR, Ragsdale SW. Controlled potential enzymology of methyl transfer reactions involved in acetyl-CoA synthesis by CO dehydrogenase and the corrinoid/iron-sulfur protein from Clostridium thermoaceticum. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39743-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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32
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M�ller-Zinkhan D, Thauer RK. Anaerobic lactate oxidation to 3 CO2 by Archaeoglobus fulgidus via the carbon monoxide dehydrogenase pathway: demonstration of the acetyl-CoA carbon-carbon cleavage reaction in cell extracts. Arch Microbiol 1990. [DOI: 10.1007/bf00249070] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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