Structural and redox plasticity in the heterodimeric periplasmic nitrate reductase
Abstract
The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme electron transfer small subunit NapB binds to the large subunit with heme II in close proximity to the [4Fe-4S] cluster of NapA. A total of 57 residues at the N- and C-terminal extremities of NapB adopt an extended conformation, embracing the NapA subunit and largely contributing to the total area of 5,900 A(2) buried in the complex. Complex formation was studied further by measuring the variation of the redox potentials of all the cofactors upon binding. The marked effects observed are interpreted in light of the three-dimensional structure and depict a plasticity that contributes to an efficient electron transfer in the complex from the heme I of NapB to the molybdenum catalytic site of NapA.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The crystal structures of NapA from Cupriavidus necator (PDB ID: 3ML1), E. coli (PDB ID: 2NYA), R. sphaeroides (PDB ID: 1OGY), and D. desulfuricans (PDB ID: 2NAP) have been reported.
“The crystal structures of NapA from several species have been reported: Cupriavidus necator (PDB ID: 3ML1),121 E. coli (PDB ID: 2NYA),96 R. sphaeroides (PDB ID: 1OGY),186 and D. desulfuricans (PDB ID: 2NAP).119”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
Tyrosine-58 in R. sphaeroides NapA participates in electron transfer from NapB to the [4Fe-4S] cluster of NapA.
“the tyrosine-58 in R. sphaeroides participates in electron transfer from NapB to the [4Fe–4S] cluster of NapA”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
Tyrosine-58 is conserved in all heterodimeric NapA but absent in monomeric NapA such as D. desulfuricans.
“conserved in all heterodimeric NapA, but absent in monomeric NapA such as D. desulfuricans.186”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
In addition to four dithiolene sulfurs, a fifth sulfur ligand derived from a conserved cysteine residue coordinates the Mo in the active site of NapA.
“In addition to four dithiolene sulfurs, a fifth sulfur ligand derived from a conserved cysteine residue coordinates the Mo in the active site of NapA.96,119,186”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
Removal of NapB from the NapAB complex reduces the efficiency of the monomer only 4-6 fold in R. sphaeroides but 30 fold in Thiosphaera pantotropha.
“Removal of NapB from the NapAB complex reduces the efficiency of the monomer only 4–6 fold in R. sphaeroides186 but 30 fold in Thiosphaera pantotropha.214”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
The NapAB complex formation may be oxidation state dependent.
“The NapAB complex formation may be oxidation state dependent as well.”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
In the reduced state the calculated Kd for the NapAB complex is ~0.5 nM, while that in the oxidized state is 2.4 μM.
“In the reduced state the calculated Kd is ~0.5 nM while that in the oxidized state is 2.4 µM.186”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
E. coli and R. sphaeroides NapAB exhibit different dissociation constants, 32 μM and 5 × 10−4 μM respectively.
“E. coli and R. sphaeroides NapAB exhibit different dissociation constants, 32 µM ref. 96 and 5 × 10−4 µM ref. 186 respectively, and are reflective of the purified form.”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
The Rhodobacter sphaeroides and Cupriavidus necator NapAB heterodimer structures have been determined using X-ray crystallography.
“The Rhodobacter sphaeroides and Cupriavidus necator NapAB heterodimer structures have been determined using X-ray crystallography.121,186”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
The N-terminus of NapB encodes a hydrophobic signal sequence, roughly 30 amino acids long, which targets unfolded NapB for periplasmic export via the sec-dependent pathway.
“The N-terminus encodes a hydrophobic signal sequence, roughly 30 amino acids long, which targets the unfolded NapB for periplasmic export via the sec dependent pathway.186,252,253”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [186]
Cites
The CCP4 suite: programs for protein crystallography
Number Collaborative Computational Project (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,299 · see citing works
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,720 · see citing works
Solvent content of protein crystals
Matthews, B. W. (1968) · Journal of Molecular Biology · doi:10.1016/0022-2836(68)90205-2 · Cited by 7,970 · see citing works
AMoRe: an automated package for molecular replacement
Navaza, J. (1994) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767393007597 · Cited by 4,941 · see citing works
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
Conte, L. L., Chothia, C., & Janin, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2439 · Cited by 1,967 · see citing works
Natural engineering principles of electron tunnelling in biological oxidation–reduction
Page, C. C., Moser, C. C., Chen, X., & Dutton, P. L. (1999) · Nature · doi:10.1038/46972 · Cited by 1,866 · see citing works
Efficient anisotropic refinement of macromolecular structures using FFT
Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S., & Dodson, E. J. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744499801405x · Cited by 937 · see citing works
Pelletier, H., & Kraut, J. (1992) · Science · doi:10.1126/science.1334573 · Cited by 677 · see citing works
Deisenhofer, J., Epp, O., Sinning, I., & Michel, H. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0097 · Cited by 612 · 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
Molybdenum and tungsten in biology
Hille, R. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02107-2 · Cited by 430 · see citing works
Crystal structure of the yeast cytochrome bc 1 complex with its bound substrate cytochrome c
Lange, C. M., & Hunte, C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052704699 · Cited by 343 · see citing works
Anderson, G. L., Williams, J. W., & Hille, R. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)35891-5 · Cited by 297 · 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
Characterization of the Reduction of Selenate and Tellurite by Nitrate Reductases
Sabaty, M., Avazéri, C., Pignol, D., & Verméglio, A. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.11.5122-5126.2001 · Cited by 210 · see citing works
Self-citationPOTTER, L. C., MILLINGTON, P., GRIFFITHS, L., THOMAS, G. H., & COLE, J. A. (1999) · Biochemical Journal · doi:10.1042/0264-6021:3440077 · Cited by 160 · see citing works
Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme
Bamford, V. A., Bruno, S., Rasmussen, T., et al. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf566 · Cited by 157 · see citing works
Axelrod, H. L., Abresch, E. C., Okamura, M. Y., Yeh, A., Rees, D. C., & Fehér, G. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00168-7 · Cited by 154 · see citing works
Une nouvelle méthode spectrophotométrique destinée à l'étude des réactions photosynthétiques
Joliot, P. A., Beal, D., & Frilley, B. (1980) · Journal de Chimie Physique · doi:10.1051/jcp/1980770209 · Cited by 146 · see citing works
Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha
Berks, B. C., RICHARDSON, D. J., Robinson, C. V., Reilly, A., Aplin, R. T., & Ferguson, S. J. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.tb18605.x · Cited by 115 · see citing works
The coordination and function of the redox centres of the membrane-bound nitrate reductases
Blasco, F., Guigliarelli, B., Magalon, A., Asso, M., Giordano, G., & Rothery, R. A. (2001) · Cellular and Molecular Life Sciences · doi:10.1007/pl00000846 · Cited by 113 · see citing works
Self-citationAssembly of membrane-bound respiratory complexes by the Tat protein-transport system
Sargent, F., Berks, B. C., & Palmer, T. (2002) · Archives of Microbiology · doi:10.1007/s00203-002-0434-2 · Cited by 88 · see citing works
Nitrate and Nitrite Utilization in Sulfate-Reducing Bacteria
Moura, I., Bursakov, S. A., Costa, C., & Moura, J. J. G. (1997) · Anaerobe · doi:10.1006/anae.1997.0093 · Cited by 84 · see citing works
Buc, J., Santini, C., Giordani, R., Czjzek, M., Wu, L., & Giordano, G. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01340.x · Cited by 83 · see citing works
Richardson, D. J., Wehrfritz, J.-M., Keech, A. M., et al. (1998) · Biochemical Society Transactions · doi:10.1042/bst0260401 · Cited by 81 · see citing works
Morelli, X., Dolla, A., Czjzek, M., et al. (2000) · Biochemistry · doi:10.1021/bi992306s · Cited by 65 · see citing works
Bennett, B., Berks, B. C., Ferguson, S. J., Thomson, A. J., & Richardson, D. J. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.00789.x · Cited by 58 · see citing works
REYES, F., GAVIRA, M., CASTILLO, F., & MORENO-VIVIÁN, C. (1998) · Biochemical Journal · doi:10.1042/bj3310897 · Cited by 56 · see citing works
Bursakov, S. A., Liu, M. Y., Payne, W. J., LeGall, J., Moura, I., & Moura, J. J. G. (1995) · Anaerobe · doi:10.1016/s1075-9964(95)80444-7 · Cited by 52 · see citing works
Morelli, X., Czjzek, M., Hatchikian, C. E., et al. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m909835199 · Cited by 48 · see citing works
Brigé, A., Leys, D., Meyer, T. E., Cusanovich, M. A., & Van Beeumen, J. J. (2002) · Biochemistry · doi:10.1021/bi012144b · Cited by 47 · see citing works
Dohse, B., Mathis, P., Wachtveitl, J., Laussermair, E., Iwata, S., Michel, H., & Oesterhelt, D. (1995) · Biochemistry · doi:10.1021/bi00036a006 · Cited by 46 · see citing works
Wachtveitl, J., Farchaus, J. W., Mathis, P., et al. (1993) · Biochemistry · doi:10.1021/bi00091a045 · Cited by 44 · see citing works
CARTRON, M. L., ROLDÁN, M. D., FERGUSON, S. J., BERKS, B. C., & RICHARDSON, D. J. (2002) · Biochemical Journal · doi:10.1042/bj20020865 · Cited by 43 · see citing works
Sabaty, M., Schwintner, C., Cahors, S., Richaud, P., & Verméglio, A. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.19.6028-6032.1999 · Cited by 29 · see citing works
Self-citationFarchaus, J. W., Wachtveitl, J., Mathis, P., et al. (1993) · Biochemistry · doi:10.1021/bi00091a044 · Cited by 27 · see citing works
Pignol, D., Adriano, J.-M., Fontecilla-Camps, J. C., & Sabaty, M. (2001) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444901015852 · Cited by 6 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
The mononuclear molybdenum enzymes
Hille, R., Hall, J., & Basu, P. (2014) · Chemical Reviews · doi:10.1021/cr400443z · Cited by 1,738 · see citing works
Nitrate and periplasmic nitrate reductases
Sparacino-Watkins, C., Stolz, J. F., & Basu, P. (2014) · Chem. Soc. Rev. · doi:10.1039/c3cs60249d · Cited by 426 · see citing works
Maia, L. B., & Moura, J. J. G. (2014) · Chemical Reviews · doi:10.1021/cr400518y · Cited by 401 · 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
The molybdenum oxotransferases and related enzymes
Hille, R. (2013) · Dalton Transactions · doi:10.1039/c2dt32376a · Cited by 133 · see citing works
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. (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
Coelho, C., González, P. J., Moura, J. G., Moura, I., Trincão, J., & João Romão, M. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.016 · Cited by 97 · see citing works
Spectroscopic studies of molybdenum and tungsten enzymes
Pushie, M. J., & George, G. N. (2011) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2011.01.056 · Cited by 86 · see citing works
To what extent do structural changes in catalytic metal sites affect enzyme function?
Valasatava, Y., Rosato, A., Furnham, N., Thornton, J. M., & Andreini, C. (2018) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2017.11.002 · Cited by 77 · see citing works
The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase
Cerqueira, N. M. F. S. A., Gonzalez, P. J., Brondino, C. D., Romão, M. J., Romão, C. C., Moura, I., & Moura, J. J. G. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21280 · Cited by 56 · see citing works
Fourmond, V., Burlat, B., Dementin, S., Arnoux, P., Sabaty, M., Boiry, S., Guigliarelli, B., Bertrand, P., Pignol, D., & Léger, C. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp807092y · Cited by 51 · 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
Kern, M., Mager, A. M., & Simon, J. (2007) · Microbiology · doi:10.1099/mic.0.2007/009928-0 · Cited by 41 · see citing works
Biaso, F., Burlat, B., & Guigliarelli, B. (2012) · Inorganic Chemistry · doi:10.1021/ic201533p · Cited by 40 · see citing works
Self-citationHofmann, M. (2009) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-009-0545-1 · Cited by 35 · see citing works
Reassessing the Strategies for Trapping Catalytic Intermediates during Nitrate Reductase Turnover
Fourmond, V., Sabaty, M., Arnoux, P., Bertrand, P., Pignol, D., & Léger, C. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911443y · Cited by 33 · see citing works
Self-citationFourmond, V., Burlat, B., Dementin, S., Sabaty, M., Arnoux, P., Étienne, É., Guigliarelli, B., Bertrand, P., Pignol, D., & Léger, C. (2010) · Biochemistry · doi:10.1021/bi902140e · Cited by 28 · see citing works
Self-citationSimpson, P. J. L., McKinzie, A. A., & Codd, R. (2010) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2010.06.002 · Cited by 20 · see citing works
- Authors
- Arnoux, P., Sabaty, M., Alric, J., Frangioni, B., Guigliarelli, B., Adriano, J.-M., & Pignol, D.
- Affiliations
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Arnoux, Pascal
- Pignol, David
- Venue
- Nature Structural & Molecular Biology
- Published
- 2003-10-05
- Volume
- 10
- Issue
- 11
- Pages
- 928-934
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2067813138
- Cited by
- 149
- References
- 37
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 7 · 2023: 5 · 2022: 5 · 2021: 5 · 2020: 9 · 2019: 7 · 2018: 5 · 2017: 4 · 2016: 3 · 2015: 5 · 2014: 7 · 2013: 13 · 2012: 4
- FWCI
- 5.99
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- European Synchrotron Radiation Facility
- Topics
- Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Hemoglobin structure and function
- Keywords
- periplasmic nitrate reductase, Rhodobacter sphaeroides, heterodimeric enzyme, denitrification, [4Fe-4S] cluster, redox potential, electron transfer, structural plasticity, protein complex structure, cofactor binding
- MeSH terms
- Kinetics, Nitrate Reductases, Oxidation-Reduction, Rhodobacter sphaeroides, Protein Structure, Tertiary, Dimerization, Protein Structure, Quaternary, Periplasmic Proteins, Nitrate Reductase
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
