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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.
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Neumann F, Dobbek H. ATP Binding and a Second Reduction Enables a Conformationally Gated Uphill Electron Transfer. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felix Neumann
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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Huening KA, Jiang R, Krzycki JA. Kinetic and substrate complex characterization of RamA, a corrinoid protein reductive activase from Methanosarcina barkeri. FEMS Microbiol Lett 2020; 367:5896951. [PMID: 32840570 DOI: 10.1093/femsle/fnaa128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/27/2020] [Indexed: 12/30/2022] Open
Abstract
In microbial corrinoid-dependent methyltransferase systems, adventitious Co(I)-corrinoid oxidation halts catalysis and necessitates repair by ATP-dependent reductive activases. RamA, an activase with a C-terminal ferredoxin domain with two [4Fe-4S] clusters from methanogenic archaea, has been far less studied than the bacterial activases bearing an N-terminal ferredoxin domain with one [2Fe-2S] cluster. These differences suggest RamA might prove to have other distinctive characteristics. Here, we examine RamA kinetics and the stoichiometry of the corrinoid protein:RamA complex. Like bacterial activases, K+ stimulates RamA. Potassium stimulation had been questioned due to differences in the primary structure of bacterial and methanogen activases. Unlike one bacterial activase, ATP is not inhibitory allowing the first determination of apparent kinetic parameters for any corrinoid activase. Unlike bacterial activases, a single RamA monomer complexes a single corrinoid protein monomer. Alanine replacement of a RamA serine residue corresponding to the serine of one bacterial activase which ligates the corrinoid cobalt during complex formation led to only moderate changes in the kinetics of RamA. These results reveal new differences in the two types of corrinoid activases, and provide direct evidence for the proposal that corrinoid activases act as catalytic monomers, unlike other enzymes that couple ATP hydrolysis to difficult reductions.
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Affiliation(s)
- Katherine A Huening
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ruisheng Jiang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Joseph A Krzycki
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA.,The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB. Appl Environ Microbiol 2019; 85:AEM.00438-19. [PMID: 31028026 DOI: 10.1128/aem.00438-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/20/2019] [Indexed: 11/20/2022] Open
Abstract
Methylmercury (MeHg) is a potent bioaccumulative neurotoxin that is produced by certain anaerobic bacteria and archaea. Mercury (Hg) methylation has been linked to the gene pair hgcAB, which encodes a membrane-associated corrinoid protein and a ferredoxin. Although microbial Hg methylation has been characterized in vivo, the cellular biochemistry and the specific roles of the gene products HgcA and HgcB in Hg methylation are not well understood. Here, we report the kinetics of Hg methylation in cell lysates of Desulfovibrio desulfuricans ND132 at nanomolar Hg concentrations. The enzymatic Hg methylation mediated by HgcAB is highly oxygen sensitive, irreversible, and follows Michaelis-Menten kinetics, with an apparent Km of 3.2 nM and V max of 19.7 fmol · min-1 · mg-1 total protein for the substrate Hg(II). Although the abundance of HgcAB in the cell lysates is extremely low, Hg(II) was quantitatively converted to MeHg at subnanomolar substrate concentrations. Interestingly, increasing thiol/Hg(II) ratios did not impact Hg methylation rates, which suggests that HgcAB-mediated Hg methylation effectively competes with cellular thiols for Hg(II), consistent with the low apparent Km Supplementation of 5-methyltetrahydrofolate or pyruvate did not enhance MeHg production, while both ATP and a nonhydrolyzable ATP analog decreased Hg methylation rates in cell lysates under the experimental conditions. These studies provide insights into the biomolecular processes associated with Hg methylation in anaerobic bacteria.IMPORTANCE The concentration of Hg in the biosphere has increased dramatically over the last century as a result of industrial activities. The microbial conversion of inorganic Hg to MeHg is a global public health concern due to bioaccumulation and biomagnification of MeHg in food webs. Exposure to neurotoxic MeHg through the consumption of fish represents a significant risk to human health and can result in neuropathies and developmental disorders. Anaerobic microbial communities in sediments and periphyton biofilms have been identified as sources of MeHg in aquatic systems, but the associated biomolecular mechanisms are not fully understood. In the present study, we investigate the biochemical mechanisms and kinetics of MeHg formation by HgcAB in sulfate-reducing bacteria. These findings advance our understanding of microbial MeHg production and may help inform strategies to limit the formation of MeHg in the environment.
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Goetzl S, Teutloff C, Werther T, Hennig SE, Jeoung JH, Bittl R, Dobbek H. Protein Dynamics in the Reductive Activation of a B12-Containing Enzyme. Biochemistry 2017; 56:5496-5502. [DOI: 10.1021/acs.biochem.7b00477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Goetzl
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Werther
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra E. Hennig
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jae-Hun Jeoung
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robert Bittl
- Fachbereich
Physik, Freie Universität Berlin, Berlin, Germany
| | - Holger Dobbek
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Berlin, Germany
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Electronic and structural properties of Cob(I)alamin: Ramifications for B 12 -dependent processes. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Schrapers P, Mebs S, Goetzl S, Hennig SE, Dau H, Dobbek H, Haumann M. Axial Ligation and Redox Changes at the Cobalt Ion in Cobalamin Bound to Corrinoid Iron-Sulfur Protein (CoFeSP) or in Solution Characterized by XAS and DFT. PLoS One 2016; 11:e0158681. [PMID: 27384529 PMCID: PMC4934906 DOI: 10.1371/journal.pone.0158681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/20/2016] [Indexed: 11/18/2022] Open
Abstract
A cobalamin (Cbl) cofactor in corrinoid iron-sulfur protein (CoFeSP) is the primary methyl group donor and acceptor in biological carbon oxide conversion along the reductive acetyl-CoA pathway. Changes of the axial coordination of the cobalt ion within the corrin macrocycle upon redox transitions in aqua-, methyl-, and cyano-Cbl bound to CoFeSP or in solution were studied using X-ray absorption spectroscopy (XAS) at the Co K-edge in combination with density functional theory (DFT) calculations, supported by metal content and cobalt redox level quantification with further spectroscopic methods. Calculation of the highly variable pre-edge X-ray absorption features due to core-to-valence (ctv) electronic transitions, XANES shape analysis, and cobalt-ligand bond lengths determination from EXAFS has yielded models for the molecular and electronic structures of the cobalt sites. This suggested the absence of a ligand at cobalt in CoFeSP in α-position where the dimethylbenzimidazole (dmb) base of the cofactor is bound in Cbl in solution. As main species, (dmb)CoIII(OH2), (dmb)CoII(OH2), and (dmb)CoIII(CH3) sites for solution Cbl and CoIII(OH2), CoII(OH2), and CoIII(CH3) sites in CoFeSP-Cbl were identified. Our data support binding of a serine residue from the reductive-activator protein (RACo) of CoFeSP to the cobalt ion in the CoFeSP-RACo protein complex that stabilizes Co(II). The absence of an α-ligand at cobalt not only tunes the redox potential of the cobalamin cofactor into the physiological range, but is also important for CoFeSP reactivation.
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Affiliation(s)
- Peer Schrapers
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Stefan Mebs
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Sebastian Goetzl
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Sandra E. Hennig
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Holger Dau
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Department of Biology, 10115, Berlin, Germany
| | - Michael Haumann
- Freie Universität Berlin, Department of Physics, 14195, Berlin, Germany
- * E-mail:
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10
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Jeoung JH, Goetzl S, Hennig SE, Fesseler J, Wörmann C, Dendra J, Dobbek H. The extended reductive acetyl-CoA pathway: ATPases in metal cluster maturation and reductive activation. Biol Chem 2014; 395:545-58. [PMID: 24477517 DOI: 10.1515/hsz-2013-0290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 11/15/2022]
Abstract
The reductive acetyl-coenzyme A (acetyl-CoA) pathway, also known as the Wood-Ljungdahl pathway, allows reduction and condensation of two molecules of carbon dioxide (CO2) to build the acetyl-group of acetyl-CoA. Productive utilization of CO2 relies on a set of oxygen sensitive metalloenzymes exploiting the metal organic chemistry of nickel and cobalt to synthesize acetyl-CoA from activated one-carbon compounds. In addition to the central catalysts, CO dehydrogenase and acetyl-CoA synthase, ATPases are needed in the pathway. This allows the coupling of ATP binding and hydrolysis to electron transfer against a redox potential gradient and metal incorporation to (re)activate one of the central players of the pathway. This review gives an overview about our current knowledge on how these ATPases achieve their tasks of maturation and reductive activation.
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ATP-induced electron transfer by redox-selective partner recognition. Nat Commun 2014; 5:4626. [PMID: 25109607 DOI: 10.1038/ncomms5626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/08/2014] [Indexed: 11/08/2022] Open
Abstract
Thermodynamically unfavourable electron transfers are enabled by coupling to an energy-supplying reaction. How the energy is transduced from the exergonic to the endergonic process is largely unknown. Here we provide the structural basis for an energy transduction process in the reductive activation of B12-dependent methyltransferases. The transfer of one electron from an activating enzyme to the cobalamin cofactor is energetically uphill and relies on coupling to an ATPase reaction. Our results demonstrate that the key to coupling is, besides the oxidation state-dependent complex formation, the conformational gating of the electron transfer. Complex formation induces a substitution of the ligand at the electron-accepting Co ion. Addition of ATP initiates electron transfer by provoking conformational changes that destabilize the complex. We show how remodelling of the electron-accepting Co(2+) promotes ATP-dependent electron transfer; an efficient strategy not seen in other electron-transferring ATPases.
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12
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Demissie TB, Repisky M, Liu H, Ruud K, Kozlowski PM. Cob(II)alamin: Relativistic DFT Analysis of the EPR Parameters. J Chem Theory Comput 2014; 10:2125-36. [DOI: 10.1021/ct400769t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Taye B. Demissie
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michal Repisky
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hui Liu
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
| | - Kenneth Ruud
- Centre for Theoretical and Computational
Chemistry, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Pawel M. Kozlowski
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, Kentucky 40292, United States
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