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Gałyńska M, de Moraes MMF, Tecmer P, Boguslawski K. Delving into the catalytic mechanism of molybdenum cofactors: a novel coupled cluster study. Phys Chem Chem Phys 2024; 26:18918-18929. [PMID: 38952220 DOI: 10.1039/d4cp01500b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
In this work, we use modern electronic structure methods to model the catalytic mechanism of different variants of the molybdenum cofactor (Moco). We investigate the dependence of various Moco model systems on structural relaxation and the importance of environmental effects for five critical points along the reaction coordinate with the DMSO and NO3- substrates. Furthermore, we scrutinize the performance of various coupled-cluster approaches for modeling the relative energies along the investigated reaction paths, focusing on several pair coupled cluster doubles (pCCD) flavors and conventional coupled cluster approximations. Moreover, we elucidate the Mo-O bond formation using orbital-based quantum information measures, which highlight the flow of σM-O bond formation and σN/S-O bond breaking. Our study shows that pCCD-based models are a viable alternative to conventional methods and offer us unique insights into the bonding situation along a reaction coordinate. Finally, this work highlights the importance of environmental effects or changes in the core and, consequently, in the model itself to elucidate the change in activity of different Moco variants.
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Affiliation(s)
- Marta Gałyńska
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Matheus Morato F de Moraes
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Paweł Tecmer
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
| | - Katharina Boguslawski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, Grudziądzka 5, 87-100 Toruń, Poland.
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Boettger JD, Neubauer C, Kopf SH, Kubicki JD. Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints. ACS EARTH & SPACE CHEMISTRY 2022; 6:2582-2594. [PMID: 36425342 PMCID: PMC9677970 DOI: 10.1021/acsearthspacechem.2c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.
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Affiliation(s)
- Jason D. Boettger
- Department
of Earth, Environmental, and Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Cajetan Neubauer
- Department
of Geological Sciences & Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
| | - Sebastian H. Kopf
- Department
of Geological Sciences & Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado 80303, United States
| | - James D. Kubicki
- Department
of Earth, Environmental, and Resource Sciences, The University of Texas at El Paso, El Paso, Texas 79968, United States
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Ingersol LJ, Yang J, Kc K, Pokhrel A, Astashkin AV, Weiner JH, Johnston CA, Kirk ML. Addressing Ligand-Based Redox in Molybdenum-Dependent Methionine Sulfoxide Reductase. J Am Chem Soc 2020; 142:2721-2725. [PMID: 31989824 DOI: 10.1021/jacs.9b11762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A combination of pulsed EPR, CW EPR, and X-ray absorption spectroscopies has been employed to probe the geometric and electronic structure of the E. coli periplasmic molybdenum-dependent methionine sulfoxide reductase (MsrP). 17O and 1H pulsed EPR spectra show that the as-isolated Mo(V) enzyme form does not possess an exchangeable H2O/OH- ligand bound to Mo as found in the sulfite oxidizing enzymes of the same family. The nature of the unusual CW EPR spectrum has been re-evaluated in light of new data on the MsrP-N45R variant and related small-molecule analogues of the active site. These data point to a novel "thiol-blocked" [(PDT)MoVO(SCys)(thiolate)]- structure, which is supported by new EXAFS data. We discuss these new results in the context of ligand-based and metal-based redox chemistry in the enzymatic oxygen atom transfer reaction.
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Affiliation(s)
- Laura J Ingersol
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Jing Yang
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Khadanand Kc
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Amrit Pokhrel
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Andrei V Astashkin
- Department of Chemistry Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Joel H Weiner
- Department of Biochemistry , University of Alberta , 474 Medical Science Building , Edmonton , Alberta T6G 2H7 , Canada
| | - Christopher A Johnston
- Department of Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
| | - Martin L Kirk
- Department of Chemistry and Chemical Biology , The University of New Mexico , MSC03 2060, 1 University of New Mexico , Albuquerque , New Mexico 87131-0001 , United States
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Xie H, Liu C, Chen X, Lei Q, Fang W, Zhou T. Theoretically exploring the key role of the Lys412 residue in the conversion of N2O to N2by nitrous oxide reductase from Achromobacter cycloclastes. NEW J CHEM 2015. [DOI: 10.1039/c5nj01339a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The active CuZcluster of NOR provides strong back-donation to coordinated N2O and activates the O atom of the N2O group facilitating H-bonding and protonationviathe Lys412 residue.
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Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Chengcheng Liu
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Xuelin Chen
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
| | - Qunfang Lei
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Wenjun Fang
- Department of Chemistry
- Zhejiang University
- Hangzhou 310027
- People's Republic of China
| | - Tao Zhou
- Department of Applied Chemistry
- Zhejiang Gongshang University
- Hangzhou 310018
- People's Republic of China
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6
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 441] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J Biol Inorg Chem 2013; 18:175-181. [PMID: 23183892 DOI: 10.1007/s00775-012-0961-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/13/2012] [Indexed: 01/12/2023]
Abstract
Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Oxygenolysis reaction mechanism of copper-dependent quercetin 2,3-dioxygenase: A density functional theory study. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4729-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Majumdar A, Sarkar S. Bioinorganic chemistry of molybdenum and tungsten enzymes: A structural–functional modeling approach. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2010.11.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gates AJ, Kemp GL, To CY, Mann J, Marritt SJ, Mayes AG, Richardson DJ, Butt JN. The relationship between redox enzyme activity and electrochemical potential—cellular and mechanistic implications from protein film electrochemistry. Phys Chem Chem Phys 2011; 13:7720-31. [DOI: 10.1039/c0cp02887h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Fourmond V, Sabaty M, Arnoux P, Bertrand P, Pignol D, Léger C. Reassessing the Strategies for Trapping Catalytic Intermediates during Nitrate Reductase Turnover. J Phys Chem B 2010; 114:3341-7. [DOI: 10.1021/jp911443y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Vincent Fourmond
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Monique Sabaty
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Pascal Arnoux
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Patrick Bertrand
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - David Pignol
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Christophe Léger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
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15
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Xie H, Cao Z. Enzymatic Reduction of Nitrate to Nitrite: Insight from Density Functional Calculations. Organometallics 2009. [DOI: 10.1021/om9008197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Hujun Xie
- Department of Applied Chemistry, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310035, People's Republic of China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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16
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The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. J Comput Chem 2009; 30:2466-84. [DOI: 10.1002/jcc.21280] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Ryde U, Schulzke C, Starke K. Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study. J Biol Inorg Chem 2009; 14:1053-64. [PMID: 19479286 PMCID: PMC3085732 DOI: 10.1007/s00775-009-0548-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 05/01/2009] [Indexed: 11/29/2022]
Abstract
A density functional theory study of the influence of the various functional groups of the molybdopterin ligand on electronic and geometric properties of active-site models for the molybdenum and tungsten cofactors has been undertaken. We used analogous molybdenum and tungsten complexes with increasingly accurate representation of the molybdopterin ligands and compared bond lengths, angles, charge distribution, composition of the binding orbitals, as well as the redox potentials in relation to each other. On the basis of our findings, we suggest using ligand systems including the pyrane and the pyrazine rings, besides the dithiolene function, to obtain sufficiently reliable computational, but also synthetic, models for the molybdenum and tungsten cofactors, whereas the second ring of the pterin might be neglected for efficiency reasons.
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Affiliation(s)
- Ulf Ryde
- Department of Theoretical Chemistry, Chemical Center, Lund University, 124, 221 00 Lund, Sweden
| | - Carola Schulzke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
| | - Kerstin Starke
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstr. 4, 37077 Göttingen, Germany
- Department of Chemical Physics, Chemical Center, Lund University, 124, 221 00 Lund, Sweden
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18
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Antony S, Bayse CA. Theoretical Studies of Models of the Active Site of the Tungstoenzyme Acetylene Hydratase. Organometallics 2009. [DOI: 10.1021/om900230x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonia Antony
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529
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Hofmann M. Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA. J Biol Inorg Chem 2009; 14:1023-35. [DOI: 10.1007/s00775-009-0545-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
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21
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Bayse CA. Density-functional theory models of xanthine oxidoreductase activity: comparison of substrate tautomerization and protonation. Dalton Trans 2009:2306-14. [DOI: 10.1039/b821878a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Pal K, Sarkar S. The Role of Axial Ligation in Nitrate Reductase: A Model Study by DFT Calculations on the Mechanism of Nitrate Reduction. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800514] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Cheng M, Bakac A. Photochemical Oxidation of Halide Ions by a Nitratochromium(III) Complex. Kinetics, Mechanism, and Intermediates. J Am Chem Soc 2008; 130:5600-5. [DOI: 10.1021/ja8000453] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingming Cheng
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Andreja Bakac
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
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Najmudin S, González PJ, Trincão J, Coelho C, Mukhopadhyay A, Cerqueira NMFSA, Romão CC, Moura I, Moura JJG, Brondino CD, Romão MJ. Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum. J Biol Inorg Chem 2008; 13:737-53. [PMID: 18327621 DOI: 10.1007/s00775-008-0359-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 02/21/2008] [Indexed: 11/30/2022]
Abstract
Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.
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Affiliation(s)
- Shabir Najmudin
- Departamento de Química, FCT-UNL, REQUIMTE/CQFB, Monte de Caparica, 2829-516, Almada, Portugal.
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