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Wiley S, Griffith C, Eckert P, Mueller AP, Nogle R, Simpson SD, Köpke M, Can M, Sarangi R, Kubarych K, Ragsdale SW. An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation. J Biol Chem 2024; 300:107503. [PMID: 38944127 PMCID: PMC11321310 DOI: 10.1016/j.jbc.2024.107503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/05/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
One of the seven natural CO2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.
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Affiliation(s)
- Seth Wiley
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Claire Griffith
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter Eckert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Mehmet Can
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Kubarych
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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2
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Gencic S, Duin EC, Grahame DA. The two-electron reduced A cluster in acetyl-CoA synthase: Preparation, characteristics and mechanistic implications. J Inorg Biochem 2023; 240:112098. [PMID: 36580832 DOI: 10.1016/j.jinorgbio.2022.112098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Acetyl-CoA synthase (ACS) is a central enzyme in the carbon and energy metabolism of certain anaerobic species of bacteria and archaea that catalyzes the direct synthesis and cleavage of the acetyl CC bond of acetyl-CoA by an unusual enzymatic mechanism of special interest for its use of organonickel intermediates. An Fe4S4 cluster associated with a proximal, reactive Nip and distal spectator Nid comprise the active site metal complex, known as the A cluster. Experimental and theoretical methods have uncovered much about the ACS mechanism, but have also opened new unanswered questions about the structure and reactivity of the A cluster in various intermediate forms. Here we report a method for large scale isolation of ACS with its A cluster in the acetylated state. Isolated acetyl-ACS and the two-electron reduced ACS, produced by acetyl-ACS reaction with CoA, were characterized by UV-visible and EPR spectroscopy. Reactivity with electron acceptors provided an assessment of the apparent Em for two-electron reduction of the A cluster. The results help to distinguish between alternative electronic states of the reduced cluster, provide evidence for a role of the Fe/S cluster in catalysis, and offer an explanation of why one-electron reductive activation is observed for a reaction cycle involving 2-electron chemistry.
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Affiliation(s)
- Simonida Gencic
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA.
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3
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Elghobashi-Meinhardt N, Tombolelli D, Mroginski MA. QM/MM computations reveal details of the acetyl-CoA synthase catalytic center. Biochim Biophys Acta Gen Subj 2020; 1864:129579. [DOI: 10.1016/j.bbagen.2020.129579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/31/2020] [Accepted: 02/22/2020] [Indexed: 10/24/2022]
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4
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Yoshiya K, Sato T, Omori S, Maruyama S. The Birthplace of Proto-Life: Role of Secondary Minerals in Forming Metallo-Proteins through Water-Rock Interaction of Hadean Rocks. ORIGINS LIFE EVOL B 2018; 48:373-393. [PMID: 30945039 DOI: 10.1007/s11084-019-09571-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/22/2019] [Indexed: 10/27/2022]
Abstract
The surface of Hadean Earth was mainly covered with three types of rocks-komatiite, KREEP basalt and anorthosite-which were remarkably different from those on the modern Earth. The water-rock interaction between these rocks and water provided a highly reducing environment and formed secondary minerals on the surface of the rocks that are important for producing metallo-enzymes for the emergence of primordial life. Previous studies suggested a correlation between the active site of metallo-enzymes and sulfide minerals based on the affinity of their structures, but they did not discuss the origin of metallic elements contained in these minerals which is critical to understanding where life began. We investigated secondary minerals formed through water-rock interactions of komatiite in a subaerial geyser system, then discussed the relationship between the active site of metallo-enzymes and secondary minerals. Instead of komatiite, we used serpentinite collected from the Hakuba Happo area, Nagano Prefecture in central-north Japan, which is thought to be a modern analog for the Hadean environment. We found several minor minerals, such as magnetite, chromite, pyrite and pentlandite in addition to serpentine minerals. Pentlandite has not been mentioned in previous studies as one of the candidates that could supply important metallic elements to build metallo-enzymes. It has been shown to be a catalyst for hydrogen generation possibly, because of structural similarity to the active site of hydrogenases. We consider the possibility that nickel-iron sulfide, pentlandite, could be important minerals for the origin of life. In addition, we estimated what kinds of minor minerals would be obtained from the water-rock interaction of these rocks using thermodynamic calculations. KREEP basalt contains a large amount of iron and it could be useful for producing metallo-enzymes, especially ferredoxins-electron transfer enzymes, which may have assisted in the emergence of life.
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Affiliation(s)
- Kazumi Yoshiya
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Tomohiko Sato
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Soichi Omori
- The Open University of Japan, 2-11 Wakaba, Mihama-ku, Chiba, 261- 8586, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Novosibirsk State University, Novosibirsk, 630090, Russia
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5
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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6
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Schrapers P, Ilina J, Gregg CM, Mebs S, Jeoung JH, Dau H, Dobbek H, Haumann M. Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy. PLoS One 2017; 12:e0171039. [PMID: 28178309 PMCID: PMC5298270 DOI: 10.1371/journal.pone.0171039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/13/2017] [Indexed: 11/18/2022] Open
Abstract
Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.
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Affiliation(s)
- Peer Schrapers
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Julia Ilina
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina M. Gregg
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institute of Biology, Structural Biology/Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Berlin, Germany
- * E-mail:
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7
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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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Horn B, Limberg C, Herwig C, Mebs S. The conversion of nickel-bound CO into an acetyl thioester: organometallic chemistry relevant to the acetyl coenzyme A synthase active site. Angew Chem Int Ed Engl 2011; 50:12621-5. [PMID: 22065604 DOI: 10.1002/anie.201105281] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/02/2011] [Indexed: 11/06/2022]
Abstract
When three become one: Within one nickel-based model system, the three reactants CO, MeI, and PhSH have been assembled to yield an acetyl thioester. The reactivity is of relevance for the functioning of the acetyl coenzyme A synthase active site and provides insights into possible binding sequences.
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Affiliation(s)
- Bettina Horn
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Straße 2, 12489 Berlin, Germany
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9
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Horn B, Limberg C, Herwig C, Mebs S. Die Umsetzung von nickelgebundenem CO zum Thioester: Organometallchemie mit Bezug zum aktiven Zentrum der Acetyl-Coenzym-A-Synthase. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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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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11
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Gencic S, Duin EC, Grahame DA. Tight coupling of partial reactions in the acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex from Methanosarcina thermophila: acetyl C-C bond fragmentation at the a cluster promoted by protein conformational changes. J Biol Chem 2010; 285:15450-15463. [PMID: 20202935 DOI: 10.1074/jbc.m109.080994] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Direct synthesis and cleavage of acetyl-CoA are carried out by the bifunctional CO dehydrogenase/acetyl-CoA synthase enzyme in anaerobic bacteria and by the acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex in Archaea. In both systems, a nickel- and Fe/S-containing active site metal center, the A cluster, catalyzes acetyl C-C bond formation/breakdown. Carbonyl group exchange of [1-(14)C]acetyl-CoA with unlabeled CO, a hallmark of CODH/ACS, is weakly active in ACDS, and exchange with CO(2) was up to 350 times faster, indicating tight coupling of CO release at the A cluster to CO oxidation to CO(2) at the C cluster in CO dehydrogenase. The basis for tight coupling was investigated by analysis of three recombinant A cluster proteins, ACDS beta subunit from Methanosarcina thermophila, acetyl-CoA synthase of Carboxydothermus hydrogenoformans (ACS(Ch)), and truncated ACS(Ch) lacking its 317-amino acid N-terminal domain. A comparison of acetyl-CoA synthesis kinetics, CO exchange, acetyltransferase, and A cluster Ni(+)-CO EPR characteristics demonstrated a direct role of the ACS N-terminal domain in promoting acetyl C-C bond fragmentation. Protein conformational changes, related to "open/closed" states previously identified crystallographically, were indicated to have direct effects on the coordination geometry and stability of the A cluster Ni(2+)-acetyl intermediate, controlling Ni(2+)-acetyl fragmentation and Ni(2+)(CO)(CH(3)) condensation. EPR spectral changes likely reflect variations in the Ni(+)-CO equatorial coordination environment in closed buried hydrophobic and open solvent-exposed states. The involvement of subunit-subunit interactions in ACDS, versus interdomain contacts in ACS, ensures that CO is not released from the ACDS beta subunit in the absence of appropriate interactions with the alpha(2)epsilon(2) CO dehydrogenase component. The resultant high efficiency CO transfer explains the low rate of CO exchange relative to CO(2).
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Affiliation(s)
- Simonida Gencic
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Evert C Duin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814.
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12
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Matsumoto T, Ito M, Kotera M, Tatsumi K. A dinuclear nickel complex modeling of the Nid(ii)-Nip(i) state of the active site of acetyl CoA synthase. Dalton Trans 2010; 39:2995-7. [DOI: 10.1039/b924915j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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