The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase
Open accessAbstract
The catalytic mechanism of nitrate reduction by periplasmic nitrate reductases has been investigated using theoretical and computational means. We have found that the nitrate molecule binds to the active site with the Mo ion in the +6 oxidation state. Electron transfer to the active site occurs only in the proton‐electron transfer stage, where the Mo V species plays an important role in catalysis. The presence of the sulfur atom in the molybdenum coordination sphere creates a pseudo‐dithiolene ligand that protects it from any direct attack from the solvent. Upon the nitrate binding there is a conformational rearrangement of this ring that allows the direct contact of the nitrate with Mo VI ion. This rearrangement is stabilized by the conserved methionines Met141 and Met308. The reduction of nitrate into nitrite occurs in the second step of the mechanism where the two dimethyl‐dithiolene ligands have a key role in spreading the excess of negative charge near the Mo atom to make it available for the chemical reaction. The reaction involves the oxidation of the sulfur atoms and not of the molybdenum as previously suggested. The mechanism involves a molybdenum and sulfur‐based redox chemistry instead of the currently accepted redox chemistry based only on the Mo ion. The second part of the mechanism involves two protonation steps that are promoted by the presence of Mo V species. Mo VI intermediates might also be present in this stage depending on the availability of protons and electrons. Once the water molecule is generated only the Mo VI species allow water molecule dissociation, and, the concomitant enzymatic turnover. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
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The mechanistic proposal for the persulfide bond was corroborated by density functional theory calculations.
“The mechanistic proposal was corroborated by density functional theory calculations. 202,203”
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Density-functional thermochemistry. III. The role of exact exchange
Becke, A. D. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464913 · Cited by 103,767 · see citing works
Lee, C., Yang, W., & Parr, R. G. (1988) · Physical Review B · doi:10.1103/physrevb.37.785 · Cited by 100,874 · see citing works
Stephens, P. J., Devlin, F. J., Chabalowski, C. F., & Frisch, M. J. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100096a001 · Cited by 23,329 · see citing works
Vosko, S. H., Wilk, L., & Nusair, M. (1980) · Canadian Journal of Physics · doi:10.1139/p80-159 · Cited by 20,807 · see citing works
Hay, P. J., & Wadt, W. R. (1985) · The Journal of Chemical Physics · doi:10.1063/1.448975 · Cited by 15,622 · see citing works
The mononuclear molybdenum enzymes
Hille, R., Hall, J., & Basu, P. (2014) · Chemical Reviews · doi:10.1021/cr400443z · Cited by 1,738 · see citing works
The Mononuclear Molybdenum Enzymes
Hille, R. (1996) · Chemical Reviews · doi:10.1021/cr950061t · Cited by 1,501 · see citing works
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
Petřek, M., Otyepka, M., Banáš, P., Košinová, P., Koča, J., & Damborský, J. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-316 · Cited by 523 · see citing works
Functional, biochemical and genetic diversity of prokaryotic nitrate reductases
Richardson, D. J., Berks, B. C., Russell, D. A., Spiro, S., & Taylor, C. J. (2001) · Cellular and Molecular Life Sciences · doi:10.1007/pl00000845 · Cited by 466 · see citing works
Crystal structure of the first dissimilatory nitrate reductase at 1.9 Å solved by MAD methods
Dias, J. M., Than, M. E., Humm, A., Huber, R., Bourenkov, G. P., Bartunik, H. D., Bursakov, S., Calvete, J., Caldeira, J., Carneiro, C., et al. (1999) · Structure · doi:10.1016/s0969-2126(99)80010-0 · Cited by 286 · see citing works
Self-citationBacterial nitrate reductases: Molecular and biological aspects of nitrate reduction
González, P. J., Correia, C., Moura, I., Brondino, C. D., & Moura, J. J. G. (2006) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2005.11.024 · Cited by 273 · see citing works
Self-citationQuantum chemical modeling of enzyme active sites and reaction mechanisms
Himo, F. (2005) · Theoretical Chemistry Accounts · doi:10.1007/s00214-005-0012-1 · Cited by 199 · see citing works
Raaijmakers, H. C. A., Macieira, S., Dias, J. M. L., Teixeira, S. C. M., Bursakov, S. A., Huber, R., Moura, J. J. G., Moura, I., & Romão, M. J. (2002) · Structure · doi:10.1016/s0969-2126(02)00826-2 · Cited by 186 · see citing works
Self-citationRaaijmakers, H. C. A., & Romão, M. J. (2006) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-006-0129-2 · Cited by 167 · see citing works
Self-citationFischer-Schrader, K., Barbier, G. G., Hecht, H. J., Mendel, R. R., Campbell, W. H., & Schwarz, G. (2005) · The Plant Cell · doi:10.1105/tpc.104.029694 · Cited by 157 · see citing works
Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase
Arnoux, P., Sabaty, M., Alric, J., Frangioni, B., Guigliarelli, B., Adriano, J.-M., & Pignol, D. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb994 · Cited by 149 · see citing works
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases
Moura, J. J. G., Brondino, C. D., Trinc�o, J., & Rom�o, M. J. (2004) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-004-0573-9 · Cited by 141 · see citing works
Self-citationJepson, B. J. N., Mohan, S., Clarke, T. A., Gates, A. J., Cole, J. A., Butler, C. S., Butt, J. N., Hemmings, A. M., & Richardson, D. J. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m607353200 · Cited by 120 · see citing works
Najmudin, S., González, P. J., Trincão, J., Coelho, C., Mukhopadhyay, A., Cerqueira, N. M. F. S. A., Romão, C. C., Moura, I., Moura, J. J. G., Brondino, C. D., et al. (2008) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-008-0359-6 · Cited by 116 · see citing works
Self-citationButler, C. S., Charnock, J. M., Bennett, B., Sears, H. J., Reilly, A. J., Ferguson, S. J., Garner, C. D., Lowe, D. J., Thomson, A. J., Berks, B. C., et al. (1999) · Biochemistry · doi:10.1021/bi990402n · Cited by 99 · see citing works
Tuning a Nitrate Reductase for Function
Jepson, B. J. N., Anderson, L. J., Rubio, L. M., Taylor, C. J., Butler, C. S., Flores, E., Antonia Herrero, B., Butt, J. N., & Richardson, D. J. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m402669200 · Cited by 79 · see citing works
Leopoldini, M., Russo, N., Toscano, M., Dułak, M., & Wesołowski, T. A. (2006) · Chemistry - A European Journal · doi:10.1002/chem.200500790 · Cited by 74 · see citing works
Frangioni, B., Arnoux, P., Sabaty, M., Pignol, D., Bertrand, P., Guigliarelli, B., & Léger, C. (2004) · Journal of the American Chemical Society · doi:10.1021/ja0384072 · Cited by 70 · see citing works
Chemical keys to molybdenum enzymes *
Stiefel, E. I. (1997) · Journal of the Chemical Society Dalton Transactions · doi:10.1039/a704936f · Cited by 65 · see citing works
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
Damborský, J., Petřek, M., Banáš, P., & Otyepka, M. (2006) · Biotechnology Journal · doi:10.1002/biot.200600208 · Cited by 59 · see citing works
Dehydration of Ribonucleotides Catalyzed by Ribonucleotide Reductase: The Role of the Enzyme
Cerqueira, N. M. F. S. A., Fernandes, P. A., Eriksson, L. A., & Ramos, M. J. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.054627 · Cited by 49 · see citing works
Self-citationBrondino, C. D., Rivas, M. G., Romão, M. J., Moura, J. J. G., & Moura, I. (2006) · Accounts of Chemical Research · doi:10.1021/ar050104k · Cited by 49 · see citing works
Self-citationGonzález, P. J., Rivas, M. G., Brondino, C. D., Bursakov, S. A., Moura, I., & Moura, J. J. G. (2006) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-006-0110-0 · Cited by 45 · see citing works
Self-citationHofmann, M. (2007) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-007-0271-5 · Cited by 29 · see citing works
New insights into a critical biological control step of the mechanism of Ribonucleotide reductase
Cerqueira, N. M. F. S. A., Fernandes, P. A., Eriksson, L. A., & Ramos, M. J. (2004) · Journal of Molecular Structure THEOCHEM · doi:10.1016/j.theochem.2003.10.073 · Cited by 18 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 30
- Moura, J. J. G.; Brondino, C. D.; Trincao, J.; Romao, M. J. J Biol Inorg Chem 2004, 9, 791.
- Gonzalez, P. J.; Correia, C.; Moura, I.; Brondino, C. D.; Moura, J. J. G. J Inorg Biochem 2006, 100, 1015.
- Hille, R. Chem Rev 1996, 96, 2757.
- Richardson, D. J.; Berks, B. C.; Russell, D. A.; Spiro, S.; Taylor, C. J. Cell Mol Life Sci 2001, 58, 165.
- Fischer, K.; Barbier, G. G.; Hecht, H. J.; Mendel, R. R.; Campbell, W. H.; Schwarz, G. Plant Cell 2005, 17, 1167.
- Dias, J. M.; Than, M. E.; Humm, A.; Huber, R.; Bourenkov, G. P.; Bartunik, H. D.; Bursakov, S.; Calvete, J.; Caldeira, J.; Carneiro, C.; Moura, J. J. G.; Moura, I.; Romao, M. J. Structure 1999, 7, 65.
- Arnoux, P.; Sabaty, M.; Alric, J.; Frangioni, B.; Guigliarelli, B.; Adriano, J. M.; Pignol, D. Nat Struct Biol 2003, 10, 928.
- Jepson, B. J. N.; Mohan, S.; Clarke, T. A.; Gates, A. J.; Cole, J. A.; Butler, C. S.; Butt, J. N.; Hemmings, A. M.; Richardson, D. J. J Biol Chem 2007, 282, 6425.
- Najmudin, S.; Gonzalez, P. J.; Trincao, J.; Coelho, C.; Mukhopad- hyay, A.; Cerqueira, N. M. F. S. A.; Romao, C. C.; Moura, I.; Moura, J. J. G.; Brondino, C. D.; Romao, M. J. J Biol Inorg Chem 2008, 13, 737.
- Raaijmakers, H.; Macieira, S.; Dias, J. M.; Teixeira, S.; Bursakov, S.; Huber, R.; Moura, J. J. G.; Moura, I.; Romao, M. J. Structure 2002, 10, 1261.
- Raaijmakers, H. C. A.; Romao, M. J. J Biol Inorg Chem 2006, 11, 849.
- Becke, A. D. J Chem Phys 1993, 98, 5648.
- Lee, C. T.; Yang, W. T.; Parr, R. G. Phys Rev B 1988, 37, 785.
- Vosko, S. H.; Wilk, L.; Nusair, M. Can J Phys 1980, 58, 1200.
- Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J Phys Chem 1994, 98, 11623.
- Hay, P. J.; Wadt, W. R. J Chem Phys 1985, 82, 299.
- Cerqueira, N. M. F. S. A.; Femandes, P. A.; Eriksson, L. A.; Ramos, M. J. J Mol Struc-Theochem 2004, 709, 53.
- Cerqueira, N. M. F. S. A.; Fernandes, P. A.; Eriksson, L. A.; Ramos, M. J. Biophys J 2006, 90, 2109.
- Himo, F. Theor Chem Acc 2006, 116, 232.
- Brondino, C. D.; Rivas, M. G.; Romao, M. J.; Moura, J. J. G.; Moura, I. Acc Chem Res 2006, 39, 788.
- Gonzalez, P. J.; Rivas, M. G.; Brondino, C. D.; Bursakov, S. A.; Moura, I.; Moura, J. J. G. J Biol Inorg Chem 2006, 11, 609.
- Frangioni, B.; Arnoux, P.; Sabaty, M.; Pignol, D.; Bertrand, P.; Guigliarelli, B.; Leger, C. J Am Chem Soc 2004, 126, 1328.
- Jepson, B. J. N.; Anderson, L. J.; Rubio, L. M.; Taylor, C. J.; Butler, C. S.; Flores, E.; Herrero, A.; Butt, J. N.; Richardson, D. J. J Biol Chem 2004, 279, 32212.
- Petr ˇek, M.; Otyepka, M.; Bana ´s ˇ, P.; Kos ˇsinova ´, P.; Koc ˇa, J.; Dam- borsky ´, J. BMC Bioinformatics 2006, 7, 316.
- Damborsky ´, J.; Petr ˇek, M.; Bana ´s ˇ, P.; Otyepka, M. Biotechnol J 2007, 2, 62.
- Damborsky ´, J.; Petr ˇek, M.; Bana ´s ˇ, P.; Otyepka, M. Biotechnol J 2007, 2, 62.
- Butler, C. S.; Charnock, J. M.; Bennett, B.; Sears, H. J.; Reilly, A. J.; Ferguson, S. J.; Garner, C. D.; Lowe, D. J.; Thomson, A. J.; Berks, B. C.; Richardson, D. J. Biochem 1999, 38, 9000.
- Leopoldini, M.; Russo, N.; Toscano, M.; Dulak, M.; Wesolowski, T. A. Chemistry-Eur J 2006, 12, 2532.
- Hofmann, M. J Biol Inorg Chem 2007, 12, 989.
- Stiefel, E. I. J Chem Soc Dalton Trans 1997, 21, 3915.
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Marques, H. M. (2025) · Inorganics · doi:10.3390/inorganics13070219 · Cited by 6 · see citing works
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Srivastava, A. P., Knaff, D. B., & Setif, P. Q. Y. (2014) · Biochemistry · doi:10.1021/bi500386n · Cited by 6 · see citing works
Pterin-Containing Microbial Molybdenum Enzymes
Metzger, M. C., & Basu, P. (2022) · Advances in environmental microbiology · doi:10.1007/978-3-030-97185-4_13 · Cited by 5 · see citing works
Mononuclear Molybdenum-Containing Enzymes
Maia, L. B., & Moura, J. J. G. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.13932-0 · Cited by 4 · see citing works
Self-citationRichardson, D. J. (2025) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2025.07.004 · Cited by 3 · see citing works
Molybdenum- and Tungsten-Mediated Oxidations
Schulzke, C. (2013) · Elsevier eBooks · doi:10.1016/b978-0-08-097774-4.00926-8 · Cited by 3 · see citing works
Structure and function of periplasmic nitrate reductase
Mongkonpruthangkoon, C., Giri, N. C., & Basu, P. (2026) · Biochemical Society Transactions · doi:10.1042/bst20250033 · Cited by 2 · see citing works
Biochemical and structural studies of human methionine synthase reductase
Xiao, L. (2010) · Research Explorer (The University of Manchester)
Characterization of molybdenum and tungsten formate dehydrogenases from sulfate reducing bacteria
Mota, C. (2011) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
- Authors
- Cerqueira, N. M. F. S. A., Gonzalez, P. J., Brondino, C. D., Romão, M. J., Romão, C. C., Moura, I., & Moura, J. J. G.
- Affiliations
- Universidade Nova de Lisboa (PT)
- Universidad Nacional del Litoral (AR)
- Corresponding author
- Cerqueira, N. M. F. S. A.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2009-04-09
- Volume
- 30
- Issue
- 15
- Pages
- 2466-2484
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2113352081
- Cited by
- 56
- References
- 30
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 3 · 2022: 2 · 2021: 1 · 2020: 4 · 2019: 2 · 2018: 3 · 2017: 2 · 2016: 2 · 2015: 7 · 2014: 6 · 2013: 6 · 2012: 4
- FWCI
- 2.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Computational Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Conicet (submittedVersion, cc-by-nc-sa)
- Funders
- Fundação para a Ciência e a Tecnologia (POCI2010)
- Topics
- Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
- Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
- Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
- Keywords
- periplasmic nitrate reductase, nitrate reduction, catalytic mechanism, molybdenum coordination, sulfur-containing ligands, proton-electron transfer, methionine residues, nitrite production, sulfur oxidation, redox chemistry, conformational change
- MeSH terms
- Catalysis, Computer Simulation, Ligands, Models, Chemical, Molybdenum, Nitrates, Organometallic Compounds, Oxidation-Reduction, Sulfhydryl Compounds, Catalytic Domain, Nitrate Reductase
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