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Cited by 286Metalloenzymes and iron-sulfur proteinsEnzyme Structure and FunctionMetal-Catalyzed Oxygenation Mechanisms

Crystal structure of the first dissimilatory nitrate reductase at 1.9 Å solved by MAD methods

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Dias, João M, Than, Manuel E, Humm, Andreas, Huber, Robert, Bourenkov, Gleb P, Bartunik, Hans D, Bursakov, Sergey, Calvete, Juan +5 more·1999·Structure
DOI 10.1016/s0969-2126(99)80010-0
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Abstract

Background The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (MGD) cofactor and one [4Fe-4S] cluster in a single polypeptide chain of 723 amino acid residues. To date, there is no crystal structure of a nitrate reductase.Results The first crystal structure of a dissimilatory (respiratory) nitrate reductase was determined at 1.9 A resolution by multiwavelength anomalous diffraction (MAD) methods. The structure is folded into four domains with an alpha/beta-type topology and all four domains are involved in cofactor binding. The [4Fe-4S] centre is located near the periphery of the molecule, whereas the MGD cofactor extends across the interior of the molecule interacting with residues from all four domains. The molybdenum atom is located at the bottom of a 15 A deep crevice, and is positioned 12 A from the [4Fe-4S] cluster. The structure of NAP reveals the details of the catalytic molybdenum site, which is coordinated to two MGD cofactors, Cys140, and a water/hydroxo ligand. A facile electron-transfer pathway through bonds connects the molybdenum and the [4Fe-4S] cluster.Conclusions The polypeptide fold of NAP and the arrangement of the cofactors is related to that of Escherichia coli formate dehydrogenase (FDH) and distantly resembles dimethylsulphoxide reductase. The close structural homology of NAP and FDH shows how small changes in the vicinity of the molybdenum catalytic site are sufficient for the substrate specificity.

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  • 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 [119]

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Authors
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., Moura, I., & Romão, M. J.
Affiliations
  • Universidade Nova de Lisboa (PT)
  • Max Planck Institute of Biochemistry (DE)
  • Deutsches Elektronen-Synchrotron DESY (DE)
  • A N Bach Institute of Biochemistry (RU)
Corresponding author
Romão, Maria J
ORCID
Venue
Structure
Publisher
Elsevier BV
Published
1999-01
Volume
7
Issue
1
Pages
65-79
ISSN
0969-2126 (ISSN-L)
DOI
10.1016/s0969-2126(99)80010-0
OpenAlex
W2086606027
Cited by
286
References
68
Citations by year
2026: 3 · 2025: 7 · 2024: 5 · 2023: 2 · 2022: 7 · 2021: 5 · 2020: 8 · 2019: 5 · 2018: 5 · 2017: 3 · 2016: 8 · 2015: 7 · 2014: 12 · 2013: 13 · 2012: 5
FWCI
22.39
Type
journal article
Language
en
Open access
Licence
Locations
  • Structure (publishedVersion)
  • PubMed (publishedVersion)
  • Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (submittedVersion)
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
  • Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
Keywords
periplasmic nitrate reductase, Desulfovibrio desulfuricans, dissimilatory nitrate reduction, molybdenum enzymes, [4Fe-4S] cluster, cofactor binding, electron transfer pathway, substrate specificity
MeSH terms
Amino Acid Sequence, Cloning, Molecular, Desulfovibrio, Guanine Nucleotides, Iron-Sulfur Proteins, Models, Molecular, Molecular Sequence Data, Molybdenum, Nitrate Reductases, Organometallic Compounds, Protein Conformation, Recombinant Proteins, X-Ray Diffraction, Polymerase Chain Reaction, Sequence Alignment, Sequence Homology, Amino Acid, Protein Structure, Secondary, Crystallography, X-Ray, Nitrate Reductase

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