1
|
Biester A, Grahame DA, Drennan CL. Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Proc Natl Acad Sci U S A 2024; 121:e2410995121. [PMID: 39361653 DOI: 10.1073/pnas.2410995121] [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: 06/01/2024] [Accepted: 08/27/2024] [Indexed: 10/05/2024] Open
Abstract
Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH3+). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO2) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO2, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from Methanosarcina thermophila (MetCODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our MetCODH/ACS structure with our MetCODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.
Collapse
Affiliation(s)
- Alison Biester
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Wilson DWN, Thompson BC, Collauto A, Hooper RX, Knapp CE, Roessler MM, Musgrave RA. Mixed Valence {Ni 2+Ni 1+} Clusters as Models of Acetyl Coenzyme A Synthase Intermediates. J Am Chem Soc 2024; 146:21034-21043. [PMID: 39023163 PMCID: PMC11295191 DOI: 10.1021/jacs.4c06241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.
Collapse
Affiliation(s)
- Daniel W. N. Wilson
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, U.K.
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Benedict C. Thompson
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, U.K.
| | - Alberto Collauto
- Department
of Chemistry and Centre for Pulse EPR Spectroscopy, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Reagan X. Hooper
- Stanford
PULSE Institute, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Caroline E. Knapp
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Maxie M. Roessler
- Department
of Chemistry and Centre for Pulse EPR Spectroscopy, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Rebecca A. Musgrave
- Department
of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, U.K.
| |
Collapse
|
4
|
Ruickoldt J, Jeoung JH, Rudolph MA, Lennartz F, Kreibich J, Schomäcker R, Dobbek H. Coupling CO 2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis. Angew Chem Int Ed Engl 2024; 63:e202405120. [PMID: 38743001 DOI: 10.1002/anie.202405120] [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: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024]
Abstract
The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.
Collapse
Affiliation(s)
- Jakob Ruickoldt
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Maik Alexander Rudolph
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Frank Lennartz
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489, Berlin, Germany
| | - Julian Kreibich
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| | - Reinhard Schomäcker
- Technische Universität Berlin, Institut für Chemie - Technische Chemie, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany
| |
Collapse
|
5
|
Quiroz M, Jana M, Liu K, Bhuvanesh N, Hall MB, Darensbourg MY. Site specific redox properties in ligand differentiated di-nickel complexes inspired by the acetyl CoA synthase active site. Dalton Trans 2024; 53:7414-7423. [PMID: 38591102 DOI: 10.1039/d4dt00306c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Bimetallic transition metal complexes with site-specific redox properties offer a versatile platform for understanding electron polarization, intramolecular electron transfer processes, and customizing electronic and magnetic properties that might impact reactivity and catalyst design. Inspired by the dissymmetric nickel sites in the Acetyl CoA Synthase (ACS) Active Site, three new bimetallic Ni(N2S2)-Ni(S2C2R2) complexes based on Ni(N2S2) metalloligand donor synthons, Nid, in mimicry of the nickel site distal to the redox-active iron sulfur cluster of ACS, and nickel dithiolene receiver units, designated as Nip, the nickel proximal to the 4Fe4S cluster, were combined to explore the influence of ligand environment on electronic structure and redox properties of each unit. The combination of synthons gave a matrix of three S-bridged dinickel complexes, characterized by X-ray crystallography, and appropriate spectroscopies. Computational modeling is connected to the electronic characteristics of the nickel donor and receiver units. This study demonstrated the intricacies of identifying sites of electrochemical redox processes, within multi-metallic systems containing non-innocent ligands.
Collapse
Affiliation(s)
- Manuel Quiroz
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, USA.
| | - Manish Jana
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, USA.
| | - Kaiyang Liu
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, USA.
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, USA.
| | - Michael B Hall
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, USA.
| | | |
Collapse
|
6
|
Guerrero-Almaraz P, Quiroz M, Rodriguez DR, Jana M, Hall MB, Darensbourg MY. Sulfur Lone Pairs Control Topology in Heterotrimetallic Complexes: An Experimental and Theoretical Study. ACS ORGANIC & INORGANIC AU 2023; 3:393-402. [PMID: 38075453 PMCID: PMC10704581 DOI: 10.1021/acsorginorgau.3c00025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 02/12/2024]
Abstract
Heterotrimetallic complexes with (N2S2)M metallodithiolates, M = Ni2+, [Fe(NO)]2+, and [Co(NO)]2+, as bidentate chelating ligands to a central trans-Cr(NO)(MeCN) unit were characterized as the first members of a new class, NiCrNi, FeCrFe, CoCrCo. The complexes exhibit a cisoid structural topology, ascribed to the stereoactivity of the available lone pair(s) on the sulfur donors, resulting in a dispersed, electropositive pocket from the N/N and N/S hydrocarbon linkers wherein the Cr-NO site is housed. Computational studies explored alternative isomers (transoid and inverted cisoid) that suggest a combination of electronic and steric effects govern the geometrical selectivity. Electrostatic potential maps readily display the dominant electronegative potential from the sulfurs which force the NO to the electropositive pocket. The available S lone pairs work in synergy with the π-withdrawing ability of NO to lift Cr out of the S4 plane toward the NO and stabilize the geometry. The metallodithiolate ligands bound to Cr(NO) thus find structural consistency across the three congeners. Although the dinitrosyl [(bme-dach)Co(NO)-Mo(NO)(MeCN)-(bme-dach)Co(MeCN)][PF6]2 (CoMoCo') analogue displays chemical noninnocence and a partial Mo-Co bond toward (N2S2)Co'(NCCH3) in an "asymmetric butterfly" topology [Guerrero-Almaraz P.Inorg. Chem.2021, 60(21 (21), ), 15975-15979], the stability of the {Cr(NO)}5 unit prohibits such bond rearrangement. Magnetism and EPR studies illustrate spin coupling across the sulfur thiolate sulfur bridges.
Collapse
Affiliation(s)
| | - Manuel Quiroz
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - David R. Rodriguez
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - Manish Jana
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | | |
Collapse
|
7
|
Fisk M, Popa R. Decorated Vesicles as Prebiont Systems (a Hypothesis). ORIGINS LIFE EVOL B 2023; 53:187-203. [PMID: 38072914 DOI: 10.1007/s11084-023-09643-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/31/2023]
Abstract
Decorated vesicles in deep, seafloor basalts form abiotically, but show at least four life-analogous features, which makes them a candidate for origin of life research. These features are a physical enclosure, carbon-assimilatory catalysts, semi-permeable boundaries, and a source of usable energy. The nanometer-to-micron-sized spherules on the inner walls of decorated vesicles are proposed to function as mineral proto-enzymes. Chemically, these structures resemble synthetic FeS clusters shown to convert CO2, CO and H2 into methane, formate, and acetate. Secondary phyllosilicate minerals line the vesicles' inner walls and can span openings in the vesicles and thus can act as molecular sieves between the vesicles' interior and the surrounding aquifer. Lastly, basalt glass in the vesicle walls takes up protons, which replace cations in the silicate framework. This results in an inward proton flux, reciprocal outward flux of metal cations, more alkaline pH inside the vesicle than outside, and production of more phyllosilicates. Such life-like features could have been exploited to move decorated vesicles toward protolife systems. Decorated vesicles are proposed as study models of prebiotic systems that are expected to have existed on the early Earth and Earth-like exoplanets. Their analysis can lead to better understanding of changes in planetary geocycles during the origin of life.
Collapse
Affiliation(s)
- Martin Fisk
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, 97330, USA.
| | - Radu Popa
- River Road Research, Tonawanda, NY, 14150, USA
| |
Collapse
|
8
|
Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
Collapse
Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| |
Collapse
|
9
|
Fujishiro T, Takaoka K. Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases. Nat Commun 2023; 14:5609. [PMID: 37709776 PMCID: PMC10502027 DOI: 10.1038/s41467-023-41289-4] [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: 06/12/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.
Collapse
Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan.
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| |
Collapse
|
10
|
Can M, Abernathy MJ, Wiley S, Griffith C, James CD, Xiong J, Guo Y, Hoffman BM, Ragsdale SW, Sarangi R. Characterization of Methyl- and Acetyl-Ni Intermediates in Acetyl CoA Synthase Formed during Anaerobic CO 2 and CO Fixation. J Am Chem Soc 2023; 145:13696-13708. [PMID: 37306669 PMCID: PMC10311460 DOI: 10.1021/jacs.3c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Indexed: 06/13/2023]
Abstract
The Wood-Ljungdahl Pathway is a unique biological mechanism of carbon dioxide and carbon monoxide fixation proposed to operate through nickel-based organometallic intermediates. The most unusual steps in this metabolic cycle involve a complex of two distinct nickel-iron-sulfur proteins: CO dehydrogenase and acetyl-CoA synthase (CODH/ACS). Here, we describe the nickel-methyl and nickel-acetyl intermediates in ACS completing the characterization of all its proposed organometallic intermediates. A single nickel site (Nip) within the A cluster of ACS undergoes major geometric and redox changes as it transits the planar Nip, tetrahedral Nip-CO and planar Nip-Me and Nip-Ac intermediates. We propose that the Nip intermediates equilibrate among different redox states, driven by an electrochemical-chemical (EC) coupling process, and that geometric changes in the A-cluster linked to large protein conformational changes control entry of CO and the methyl group.
Collapse
Affiliation(s)
- Mehmet Can
- Department
of Biochemistry, Faculty of Pharmacy, Ankara
Medipol University, Ankara 06050, Turkey
| | - Macon J. Abernathy
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Seth Wiley
- Biosciences
Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Claire Griffith
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher D. James
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jin Xiong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Stephen W. Ragsdale
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ritimukta Sarangi
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| |
Collapse
|
11
|
Selvan D, Chakraborty S. A De Novo Designed Trimeric Metalloprotein as a Ni p Model of the Acetyl-CoA Synthase. Int J Mol Sci 2023; 24:10317. [PMID: 37373464 DOI: 10.3390/ijms241210317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
We present a Nip site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys)3 binding motif. Spectroscopic and kinetic studies of ligand binding demonstrate that Ni binding stabilizes the peptide assembly and produces a terminal NiI-CO complex. When the CO-bound state is reacted with a methyl donor, a new species is quickly produced with new spectral features. While the metal-bound CO is albeit unactivated, the presence of the methyl donor produces an activated metal-CO complex. Selective outer sphere steric modifications demonstrate that the physical properties of the ligand-bound states are altered differently depending on the location of the steric modification above or below the Ni site.
Collapse
Affiliation(s)
- Dhanashree Selvan
- Department of Chemistry and Biochemistry, University of Mississippi, Coulter Hall, Oxford, MS 38677, USA
| | - Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Mississippi, Coulter Hall, Oxford, MS 38677, USA
| |
Collapse
|
12
|
Fickenscher Z, Hey-Hawkins E. Added Complexity!-Mechanistic Aspects of Heterobimetallic Complexes for Application in Homogeneous Catalysis. Molecules 2023; 28:4233. [PMID: 37241974 PMCID: PMC10224482 DOI: 10.3390/molecules28104233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Inspired by multimetallic assemblies and their role in enzyme catalysis, chemists have developed a plethora of heterobimetallic complexes for application in homogeneous catalysis. Starting with small heterobimetallic complexes with σ-donating and π-accepting ligands, such as N-heterocyclic carbene and carbonyl ligands, more and more complex systems have been developed over the past two decades. These systems can show a significant increase in catalytic activity compared with their monometallic counterparts. This increase can be attributed to new reaction pathways enabled by the presence of a second metal center in the active catalyst. This review focuses on mechanistic aspects of heterobimetallic complexes in homogeneous catalysis. Depending on the type of interaction of the second metal with the substrates, heterobimetallic complexes can be subdivided into four classes. Each of these classes is illustrated with multiple examples, showcasing the versatility of both, the types of interactions possible, and the reactions accessible.
Collapse
Affiliation(s)
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany;
| |
Collapse
|
13
|
Wang KY, Zhang J, Hsu YC, Lin H, Han Z, Pang J, Yang Z, Liang RR, Shi W, Zhou HC. Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis. Chem Rev 2023; 123:5347-5420. [PMID: 37043332 PMCID: PMC10853941 DOI: 10.1021/acs.chemrev.2c00879] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Indexed: 04/13/2023]
Abstract
Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.
Collapse
Affiliation(s)
- Kun-Yu Wang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiaqi Zhang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu-Chuan Hsu
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hengyu Lin
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zongsu Han
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Jiandong Pang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- School
of Materials Science and Engineering, Tianjin Key Laboratory of Metal
and Molecule-Based Material Chemistry, Nankai
University, Tianjin 300350, China
| | - Zhentao Yang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Rong-Ran Liang
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Wei Shi
- Department
of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry
(MOE) and Renewable Energy Conversion and Storage Center (RECAST),
College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong-Cai Zhou
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
14
|
Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
Collapse
Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
| |
Collapse
|
15
|
Kronen M, Vázquez-Campos X, Wilkins MR, Lee M, Manefield MJ. Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae. mSystems 2023; 8:e0011923. [PMID: 36943133 PMCID: PMC10134865 DOI: 10.1128/msystems.00119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.
Collapse
Affiliation(s)
- Miriam Kronen
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Beyazay T, Belthle KS, Farès C, Preiner M, Moran J, Martin WF, Tüysüz H. Ambient temperature CO 2 fixation to pyruvate and subsequently to citramalate over iron and nickel nanoparticles. Nat Commun 2023; 14:570. [PMID: 36732515 PMCID: PMC9894855 DOI: 10.1038/s41467-023-36088-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
The chemical reactions that formed the building blocks of life at origins required catalysts, whereby the nature of those catalysts influenced the type of products that accumulated. Recent investigations have shown that at 100 °C awaruite, a Ni3Fe alloy that naturally occurs in serpentinizing systems, is an efficient catalyst for CO2 conversion to formate, acetate, and pyruvate. These products are identical with the intermediates and products of the acetyl-CoA pathway, the most ancient CO2 fixation pathway and the backbone of carbon metabolism in H2-dependent autotrophic microbes. Here, we show that Ni3Fe nanoparticles prepared via the hard-templating method catalyze the conversion of H2 and CO2 to formate, acetate and pyruvate at 25 °C under 25 bar. Furthermore, the 13C-labeled pyruvate can be further converted to acetate, parapyruvate, and citramalate over Ni, Fe, and Ni3Fe nanoparticles at room temperature within one hour. These findings strongly suggest that awaruite can catalyze both the formation of citramalate, the C5 product of pyruvate condensation with acetyl-CoA in microbial carbon metabolism, from pyruvate and the formation of pyruvate from CO2 at very moderate reaction conditions without organic catalysts. These results align well with theories for an autotrophic origin of microbial metabolism under hydrothermal vent conditions.
Collapse
Affiliation(s)
- Tuğçe Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Kendra S Belthle
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Martina Preiner
- Faculty of Geosciences, Utrecht University, Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
| | - Joseph Moran
- Université de Strasbourg, CNRS, ISIS UMR 7006, Strasbourg, France
| | - William F Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
| |
Collapse
|
18
|
Biester A, Marcano-Delgado AN, Drennan CL. Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases. Biochemistry 2022; 61:2797-2805. [PMID: 36137563 PMCID: PMC9782325 DOI: 10.1021/acs.biochem.2c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO2 by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO2 as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO2-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO2, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO2 and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.
Collapse
Affiliation(s)
- Alison Biester
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Andrea N. Marcano-Delgado
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,Bio-inspired
Solar Energy Program, Canadian Institute
for Advanced Research, Toronto, ON M5G 1M1, Canada,
| |
Collapse
|
19
|
Zovko C, Krätschmer F, Schmidt S, Seifert TP, Gamer MT, Roesky PW. A Phosphine-ß-diketiminate Nickel(I)-Complex for Small Molecule Activation. Chempluschem 2022; 87:e202200288. [PMID: 36514880 DOI: 10.1002/cplu.202200288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/07/2022] [Indexed: 11/10/2022]
Abstract
A bis(diphenyl)-phosphine functionalized ß-diketimine ligand (PNac-H) was applied for the synthesis of a subvalent Ni(I) complex [PNac-Ni]. Here, the Ni(I) center is stabilized by a tetradentate PNNP-type pocket, forming a square planar coordination sphere. Subsequently, the Ni(I) complex was investigated with regard to its reactivity and the activation of small molecules. The reductive potential of Ni(I) enabled an activation of different substrate classes, such as CH2X2 (X=Br, I), I2 or Ph2E2 (E=S, Se). The ligand's design allows a stabilization of the reactive Ni(I) species while at the same time enabling activation processes due to a hemilabile coordination behavior and accessible axial coordination sites. The activation products have been characterized by single crystal X-ray diffraction, NMR and IR spectroscopy as well as elemental analysis.
Collapse
Affiliation(s)
- Christina Zovko
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Frederic Krätschmer
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Sarah Schmidt
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Tim P Seifert
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Michael T Gamer
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| | - Peter W Roesky
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstraße 15, 76131, Karlsruhe, Germany
| |
Collapse
|
20
|
Fierro CM, Smith PD, Light ME. Structure of a dinickel(II)-dithiolate bridged macrocyclic complex synthesised via a novel solvent-assisted disulfide cleavage reaction. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
21
|
Ruickoldt J, Basak Y, Domnik L, Jeoung JH, Dobbek H. On the Kinetics of CO 2 Reduction by Ni, Fe-CO Dehydrogenases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakob Ruickoldt
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Yudhajeet Basak
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Lilith Domnik
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Jae-Hun Jeoung
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099Berlin, Germany
| |
Collapse
|
22
|
Basak Y, Jeoung JH, Domnik L, Ruickoldt J, Dobbek H. Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yudhajeet Basak
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Jae-Hun Jeoung
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Lilith Domnik
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Jakob Ruickoldt
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| | - Holger Dobbek
- Institute of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin 10099, Germany
| |
Collapse
|
23
|
Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
Collapse
Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
- Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| |
Collapse
|
24
|
Affiliation(s)
- Ryan J. Witzke
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - T. Don Tilley
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
25
|
Wiedner ES, Appel AM, Raugei S, Shaw WJ, Bullock RM. Molecular Catalysts with Diphosphine Ligands Containing Pendant Amines. Chem Rev 2022; 122:12427-12474. [PMID: 35640056 DOI: 10.1021/acs.chemrev.1c01001] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Pendant amines play an invaluable role in chemical reactivity, especially for molecular catalysts based on earth-abundant metals. As inspired by [FeFe]-hydrogenases, which contain a pendant amine positioned for cooperative bifunctionality, synthetic catalysts have been developed to emulate this multifunctionality through incorporation of a pendant amine in the second coordination sphere. Cyclic diphosphine ligands containing two amines serve as the basis for a class of catalysts that have been extensively studied and used to demonstrate the impact of a pendant base. These 1,5-diaza-3,7-diphosphacyclooctanes, now often referred to as "P2N2" ligands, have profound effects on the reactivity of many catalysts. The resulting [Ni(PR2NR'2)2]2+ complexes are electrocatalysts for both the oxidation and production of H2. Achieving the optimal benefit of the pendant amine requires that it has suitable basicity and is properly positioned relative to the metal center. In addition to the catalytic efficacy demonstrated with [Ni(PR2NR'2)2]2+ complexes for the oxidation and production of H2, catalysts with diphosphine ligands containing pendant amines have also been demonstrated for several metals for many different reactions, both in solution and immobilized on surfaces. The impact of pendant amines in catalyst design continues to expand.
Collapse
|
26
|
Biester A, Dementin S, Drennan CL. Visualizing the gas channel of a monofunctional carbon monoxide dehydrogenase. J Inorg Biochem 2022; 230:111774. [PMID: 35278753 PMCID: PMC9093221 DOI: 10.1016/j.jinorgbio.2022.111774] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/31/2022] [Accepted: 02/19/2022] [Indexed: 10/31/2022]
Abstract
Carbon monoxide dehydrogenase (CODH) plays an important role in the processing of the one‑carbon gases carbon monoxide and carbon dioxide. In CODH enzymes, these gases are channeled to and from the Ni-Fe-S active sites using hydrophobic cavities. In this work, we investigate these gas channels in a monofunctional CODH from Desulfovibrio vulgaris, which is unusual among CODHs for its oxygen-tolerance. By pressurizing D. vulgaris CODH protein crystals with xenon and solving the structure to 2.10 Å resolution, we identify 12 xenon sites per CODH monomer, thereby elucidating hydrophobic gas channels. We find that D. vulgaris CODH has one gas channel that has not been experimentally validated previously in a CODH, and a second channel that is shared with Moorella thermoacetica carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS). This experimental visualization of D. vulgaris CODH gas channels lays groundwork for further exploration of factors contributing to oxygen-tolerance in this CODH, as well as study of channels in other CODHs. We dedicate this publication to the memory of Dick Holm, whose early studies of the Ni-Fe-S clusters of CODH inspired us all.
Collapse
Affiliation(s)
- Alison Biester
- Dept. of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Sébastien Dementin
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France
| | - Catherine L Drennan
- Dept. of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Dept. of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Canadian Institute for Advanced Research, Bio-inspired Solar Energy Program, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
27
|
Jeoung J, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold. Angew Chem Int Ed Engl 2022; 61:e202117000. [PMID: 35133707 PMCID: PMC9311411 DOI: 10.1002/anie.202117000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Indexed: 11/12/2022]
Abstract
Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-VCh . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-VCh catalyzes neither CO oxidation, nor CO2 reduction. The active site of CooS-VCh undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H2 O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-VCh , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.
Collapse
Affiliation(s)
- Jae‐Hun Jeoung
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Jochen Fesseler
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Lilith Domnik
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Friederike Klemke
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich PhysikArnimallee 1414195BerlinGermany
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich PhysikArnimallee 1414195BerlinGermany
| | - Holger Dobbek
- Humboldt-Universität zu BerlinInstitut für BiologieUnter den Linden 610099BerlinGermany
| |
Collapse
|
28
|
Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy. Biomolecules 2022; 12:biom12030441. [PMID: 35327633 PMCID: PMC8945911 DOI: 10.3390/biom12030441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
Metalloproteins are involved in key cell processes such as photosynthesis, respiration, and oxygen transport. However, the presence of transition metals (notably iron as a component of [Fe-S] clusters) often makes these proteins sensitive to oxygen-induced degradation. Consequently, their study usually requires strict anaerobic conditions. Although X-ray crystallography has been the method of choice for solving macromolecular structures for many years, recently electron microscopy has also become an increasingly powerful structure-solving technique. We have used our previous experience with cryo-crystallography to develop a method to prepare cryo-EM grids in an anaerobic chamber and have applied it to solve the structures of apoferritin and the 3 [Fe4S4]-containing pyruvate ferredoxin oxidoreductase (PFOR) at 2.40 Å and 2.90 Å resolution, respectively. The maps are of similar quality to the ones obtained under air, thereby validating our method as an improvement in the structural investigation of oxygen-sensitive metalloproteins by cryo-EM.
Collapse
|
29
|
Jeoung J, Fesseler J, Domnik L, Klemke F, Sinnreich M, Teutloff C, Dobbek H. Ein sich umstrukturierender [4Fe‐3S‐nO]‐Cluster in einem Kohlenmonoxid‐Dehydrogenase‐Gerüst. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jae‐Hun Jeoung
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Jochen Fesseler
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Lilith Domnik
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Friederike Klemke
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| | - Malte Sinnreich
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Christian Teutloff
- Freie Universität Berlin, Fachbereich Physik Arnimallee 14 14195 Berlin Deutschland
| | - Holger Dobbek
- Humboldt-Universität zu Berlin Institut für Biologie Unter den Linden 6 10099 Berlin Deutschland
| |
Collapse
|
30
|
Square planar Ni(II) thiosemicarbazone complexes as functional models for carbon monoxide dehydrogenase. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
31
|
Functional Conversion of Acetyl-Coenzyme a Synthase to a Nickel Superoxide Dismutase via Rational Design of Coordination Microenvironment for the Ni d-Site. Int J Mol Sci 2022; 23:ijms23052652. [PMID: 35269794 PMCID: PMC8910529 DOI: 10.3390/ijms23052652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The Nid site coordination microenvironment of a truncated acetyl-coenzyme A synthase has been designed systematically for functional conversion to a Ni-SOD-like enzyme. To this end, the first strategy is to introduce an axial histidine ligand, using mutations F598H, S594H and S594H-GP individually. The resulting three mutants obtained Ni-SOD-like activity successfully, although the catalytic activity was about 10-fold lower than in native Ni-SOD. The second strategy is to mimic the H-bond network in the second sphere coordination microenvironment of the native Ni-SOD. Two mutations based on F598H (EFG-F598H and YGP-F598H) were designed. The successful EFG-F598H exhibited ~3-fold Ni-SOD-like activity of F598H. These designed Ni-SOD-like metalloproteins were characterized by UV/Vis, EPR and Cyclic voltammetry while F598H was also characterized by X-ray protein crystallography. The pH titrations were performed to reveal the source of the two protons required for forming H2O2 in the SOD catalytic reaction. Based on all of the results, a proposed catalytic mechanism for the Ni-SOD-like metalloproteins is presented.
Collapse
|
32
|
Nicolet Y, Cherrier MV, Amara P. Radical SAM Enzymes and Metallocofactor Assembly: A Structural Point of View. ACS BIO & MED CHEM AU 2022; 2:36-52. [PMID: 37102176 PMCID: PMC10114646 DOI: 10.1021/acsbiomedchemau.1c00044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This Review focuses on the structure-function relationship of radical S-adenosyl-l-methionine (SAM) enzymes involved in the assembly of metallocofactors corresponding to the active sites of [FeFe]-hydrogenase and nitrogenase [MoFe]-protein. It does not claim to correspond to an extensive review on the assembly machineries of these enzyme active sites, for which many good reviews are already available, but instead deals with the contribution of structural data to the understanding of their chemical mechanism (Buren et al. Chem. Rev.2020, 142 ( (25), ) 11006-11012; Britt et al. Chem. Sci.2020, 11 ( (38), ), 10313-10323). Hence, we will present the history and current knowledge about the radical SAM maturases HydE, HydG, and NifB as well as what, in our opinion, should be done in the near future to overcome the existing barriers in our understanding of this fascinating chemistry that intertwine organic radicals and organometallic complexes.
Collapse
Affiliation(s)
- Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Mickael V. Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| |
Collapse
|
33
|
Theoretical Studies of Acetyl-CoA Synthase Catalytic Mechanism. Catalysts 2022. [DOI: 10.3390/catal12020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
DFT calculations were performed for the A-cluster from the enzyme Acetyl-CoA synthase (ACS). The acid constants (pKa), reduction potentials, and pH-dependent reduction potential for the A-cluster with different oxidation states and ligands were calculated. Good agreement of the reduction potentials, dependent on pH in the experiment, was obtained. On the basis of the calculations, a mechanism for the methylation reaction involving two–electron reduction and protonation on the proximal nickel atom of the reduced A-cluster is proposed.
Collapse
|
34
|
Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
Collapse
Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
35
|
OUP accepted manuscript. Metallomics 2022; 14:6549566. [DOI: 10.1093/mtomcs/mfac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
|
36
|
Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
37
|
Lee K, Choi J, Graham PM, Lee Y. Binding of carbon monoxide at a single nickel center and its oxidative reactivity toward
CO
2
and
O
2. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kunwoo Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Jonghoon Choi
- Department of Chemistry Seoul National University Seoul South Korea
| | - Peter M. Graham
- Department of Chemistry Saint Joseph's University Philadelphia Pennsylvania USA
| | - Yunho Lee
- Department of Chemistry Seoul National University Seoul South Korea
| |
Collapse
|
38
|
Jain S, Katsyv A, Basen M, Müller V. The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide. Extremophiles 2021; 26:4. [PMID: 34919167 PMCID: PMC8683389 DOI: 10.1007/s00792-021-01251-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.
Collapse
Affiliation(s)
- Surbhi Jain
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, 18059, Rostock, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| |
Collapse
|
39
|
Meneghello M, Léger C, Fourmond V. Electrochemical Studies of CO 2 -Reducing Metalloenzymes. Chemistry 2021; 27:17542-17553. [PMID: 34506631 DOI: 10.1002/chem.202102702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Indexed: 11/07/2022]
Abstract
Only two enzymes are capable of directly reducing CO2 : CO dehydrogenase, which produces CO at a [NiFe4 S4 ] active site, and formate dehydrogenase, which produces formate at a mononuclear W or Mo active site. Both metalloenzymes are very rapid, energy-efficient and specific in terms of product. They have been connected to electrodes with two different objectives. A series of studies used protein film electrochemistry to learn about different aspects of the mechanism of these enzymes (reactivity with substrates, inhibitors…). Another series focused on taking advantage of the catalytic performance of these enzymes to build biotechnological devices, from CO2 -reducing electrodes to full photochemical devices performing artificial photosynthesis. Here, we review all these works.
Collapse
Affiliation(s)
- Marta Meneghello
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Christophe Léger
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
| | - Vincent Fourmond
- CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, and, Institut Microbiologie, Bioénergies et Biotechnologie, 31 chemin J. Aiguier, 13402, Marseille Cedex 20, France
| |
Collapse
|
40
|
Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
Collapse
Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| |
Collapse
|
41
|
Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
42
|
Basu D, Gray DL, Woods TJ, Rauchfuss TB, Arrigoni F, Zampella G. Challenges in the Synthesis of Active Site Mimics for [NiFe]-Hydrogenases. Organometallics 2021; 40:3306-3312. [PMID: 37933322 PMCID: PMC10627515 DOI: 10.1021/acs.organomet.1c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the more active areas in bioorganometallic chemistry is the preparation and reactivity studies of active site mimics of the [NiFe]-hydrogenases. One area of particular recent progress involves reactions that interconvert Ni(μ-X)Fe centers for X = OH, H, CO, as described by Song et al. Such reactions illustrate new ways to access intermediates related to the Ni-R and Ni-SI states of the enzyme. Most models are derivatives of the type (diphosphine)Ni(SR)2Fe(CO)3-n(PR'3)n. In recent work, the methodology has been generalized to include FeII(diphosphine) derivatives of Ni(N2S2), where N2S22- is the tetradentate diamine-dithiolate (CH2N(CH3)CH2CH2S-)2. Indeed, models based on Ni(N2S2) have proven valuable, but these studies also highlight challenges in working with heterobimetallic complexes, specifically the tendency of some such Ni-Fe complexes to convert to homometalliic Ni-Ni derivatives. This kind of problem is not readily detected by X-ray crystallography. With this caution in mind, we argue that one series of complexes recently described in this journal are almost certainly misassigned.
Collapse
Affiliation(s)
- Debashis Basu
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Danielle L Gray
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Toby J Woods
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United State
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Giuseppe Zampella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| |
Collapse
|
43
|
Altair T, Borges LGF, Galante D, Varela H. Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents. Life (Basel) 2021; 11:777. [PMID: 34440521 PMCID: PMC8401828 DOI: 10.3390/life11080777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.
Collapse
Affiliation(s)
- Thiago Altair
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
| | - Luiz G. F. Borges
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Hamilton Varela
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
| |
Collapse
|
44
|
Abstract
Acetogens synthesize acetyl-CoA via the CO2-fixing Wood-Ljungdahl pathway. Despite their ecological and biotechnological importance, their translational regulation of carbon and energy metabolisms remains unclear. Here, we report how carbon and energy metabolisms in the model acetogen Acetobacterium woodii are translationally controlled under different growth conditions. Data integration of genome-scale transcriptomic and translatomic analyses revealed that the acetogenesis genes, including those of the Wood-Ljungdahl pathway and energy metabolism, showed changes in translational efficiency under autotrophic growth conditions. In particular, genes encoding the Wood-Ljungdahl pathway are translated at similar levels to achieve efficient acetogenesis activity under autotrophic growth conditions, whereas genes encoding the carbonyl branch present increased translation levels in comparison to those for the methyl branch under heterotrophic growth conditions. The translation efficiency of genes in the pathways is differentially regulated by 5′ untranslated regions and ribosome-binding sequences under different growth conditions. Our findings provide potential strategies to optimize the metabolism of syngas-fermenting acetogenic bacteria for better productivity. IMPORTANCE Acetogens are capable of reducing CO2 to multicarbon compounds (e.g., ethanol or 2,3-butanediol) via the Wood-Ljungdahl pathway. Given that protein synthesis in bacteria is highly energy consuming, acetogens living at the thermodynamic limit of life are inevitably under translation control. Here, we dissect the translational regulation of carbon and energy metabolisms in the model acetogen Acetobacterium woodii under heterotrophic and autotrophic growth conditions. The latter may be experienced when acetogen is used as a cell factory that synthesizes products from CO2 during the gas fermentation process. We found that the methyl and carbonyl branches of the Wood-Ljungdahl pathway are activated at similar translation levels during autotrophic growth. Translation is mainly regulated by the 5′-untranslated-region structure and ribosome-binding-site sequence. This work reveals novel translational regulation for coping with autotrophic growth conditions and provides the systematic data set, including the transcriptome, translatome, and promoter/5′-untranslated-region bioparts.
Collapse
|
45
|
Terranova U. Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO. J Biol Inorg Chem 2021; 26:617-624. [PMID: 34255144 DOI: 10.1007/s00775-021-01878-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/17/2021] [Indexed: 10/20/2022]
Abstract
The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.
Collapse
Affiliation(s)
- Umberto Terranova
- Faculty of Medicine and Health Sciences, Crewe Campus, University of Buckingham, Crewe, CW1 5DU, UK.
| |
Collapse
|
46
|
Fujishiro T, Ooi M, Takaoka K. Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion. FEBS J 2021; 288:6752-6768. [PMID: 34101368 DOI: 10.1111/febs.16062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 06/07/2021] [Indexed: 01/26/2023]
Abstract
Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.
Collapse
Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Ooi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| |
Collapse
|
47
|
Banerjee R, Lipscomb JD. Small-Molecule Tunnels in Metalloenzymes Viewed as Extensions of the Active Site. Acc Chem Res 2021; 54:2185-2195. [PMID: 33886257 DOI: 10.1021/acs.accounts.1c00058] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to the enzyme active site based upon complementary physiochemical characteristics, which allows both acquisition and orientation. However, this chemical selectivity is more difficult to rationalize for diminutive molecules that possess too narrow a range of physical characteristics to allow either precise positioning or discrimination between a substrate and an inhibitor. Foremost among these small molecules are dissolved gases such as H2, N2, O2, CO, CO2, NO, N2O, NH3, and CH4 so often encountered in metalloenzyme catalysis. Nevertheless, metalloenzymes have evolved to metabolize these small-molecule substrates with high selectivity and efficiency.The soluble methane monooxygenase enzyme (sMMO) acts upon two of these small molecules, O2 and CH4, to generate methanol as part of the C1 metabolic pathway of methanotrophic organisms. sMMO is capable of oxidizing many alternative hydrocarbon substrates. Remarkably, however, it will preferentially oxidize methane, the substrate with the fewest discriminating physical characteristics and the strongest C-H bond. Early studies led us to broadly attribute this specificity to the formation of a "molecular sieve" in which a methane- and oxygen-sized tunnel provides a size-selective route from bulk solvent to the completely buried sMMO active site. Indeed, recent cryogenic and serial femtosecond ambient temperature crystallographic studies have revealed such a route in sMMO. A detailed study of the sMMO tunnel considered here in the context of small-molecule tunnels identified in other metalloenzymes reveals three discrete characteristics that contribute to substrate selectivity and positioning beyond that which can be provided by the active site itself. Moreover, the dynamic nature of many tunnels allows an exquisite coordination of substrate binding and reaction phases of the catalytic cycle. Here we differentiate between the highly selective molecular tunnel, which allows only the one-dimensional transit of small molecules, and the larger, less-selective channels found in typical enzymes. Methods are described to identify and characterize tunnels as well as to differentiate them from channels. In metalloenzymes which metabolize dissolved gases, we posit that the contribution of tunnels is so great that they should be considered to be extensions of the active site itself. A full understanding of catalysis by these enzymes requires an appreciation of the roles played by tunnels. Such an understanding will also facilitate the use of the enzymes or their synthetic mimics in industrial or pharmaceutical applications.
Collapse
Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| |
Collapse
|
48
|
Kulik M, Mori T, Sugita Y. Multi-Scale Flexible Fitting of Proteins to Cryo-EM Density Maps at Medium Resolution. Front Mol Biosci 2021; 8:631854. [PMID: 33842541 PMCID: PMC8025875 DOI: 10.3389/fmolb.2021.631854] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Abstract
Structure determination using cryo-electron microscopy (cryo-EM) medium-resolution density maps is often facilitated by flexible fitting. Avoiding overfitting, adjusting force constants driving the structure to the density map, and emulating complex conformational transitions are major concerns in the fitting. To address them, we develop a new method based on a three-step multi-scale protocol. First, flexible fitting molecular dynamics (MD) simulations with coarse-grained structure-based force field and replica-exchange scheme between different force constants replicas are performed. Second, fitted Cα atom positions guide the all-atom structure in targeted MD. Finally, the all-atom flexible fitting refinement in implicit solvent adjusts the positions of the side chains in the density map. Final models obtained via the multi-scale protocol are significantly better resolved and more reliable in comparison with long all-atom flexible fitting simulations. The protocol is useful for multi-domain systems with intricate structural transitions as it preserves the secondary structure of single domains.
Collapse
Affiliation(s)
- Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan.,RIKEN Center for Computational Science, Kobe, Japan.,RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| |
Collapse
|
49
|
Ghosh AC, Duboc C, Gennari M. Synergy between metals for small molecule activation: Enzymes and bio-inspired complexes. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213606] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
50
|
Cohen SE, Brignole EJ, Wittenborn EC, Can M, Thompson S, Ragsdale SW, Drennan CL. Negative-Stain Electron Microscopy Reveals Dramatic Structural Rearrangements in Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase. Structure 2021; 29:43-49.e3. [PMID: 32937101 PMCID: PMC7796957 DOI: 10.1016/j.str.2020.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
Abstract
The Ni-Fe-S-containing A-cluster of acetyl-coenzyme A (CoA) synthase (ACS) assembles acetyl-CoA from carbon monoxide (CO), a methyl group (CH3+), and CoA. To accomplish this feat, ACS must bind CoA and interact with two other proteins that contribute the CO and CH3+, respectively: CO dehydrogenase (CODH) and corrinoid Fe-S protein (CFeSP). Previous structural data show that, in the model acetogen Moorella thermoacetica, domain 1 of ACS binds to CODH such that a 70-Å-long internal channel is created that allows CO to travel from CODH to the A-cluster. The A-cluster is largely buried and is inaccessible to CFeSP for methylation. Here we use electron microscopy to capture multiple snapshots of ACS that reveal previously uncharacterized domain motion, forming extended and hyperextended structural states. In these structural states, the A-cluster is accessible for methylation by CFeSP.
Collapse
Affiliation(s)
- Steven E Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Elizabeth C Wittenborn
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mehmet Can
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Samuel Thompson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1.
| |
Collapse
|