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Cited by 47Enzyme Structure and FunctionMetalloenzymes and iron-sulfur proteinsHemoglobin structure and function

The 1.25 Å Resolution Structure of the Diheme NapB Subunit of Soluble Nitrate Reductase Reveals a Novel Cytochrome c Fold with a Stacked Heme Arrangement,

Brigé, Ann, Leys, David, Meyer, Terrance E., Cusanovich, Michael A., Van Beeumen, Jozef J.·2002·Biochemistry
DOI 10.1021/bi012144b
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Abstract

The diheme cytochrome NapB constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. The NapB protein is essential in transferring electrons to the large catalytic subunit NapA, which subsequently reduces nitrate to nitrite. Here we present the crystal structure of a proteolyzed form of recombinant NapB from Haemophilus influenzae, which was determined by the multiple-wavelength anomalous dispersion (MAD) method at 1.25 A resolution. This structure shows an unprecedented fold, confirming that NapB proteins belong to a new class of cytochromes. The two heme groups have nearly parallel heme planes and are stacked at van der Waals distances with an iron-to-iron distance of only 9.9 A, two structural features that are also present in the split-Soret diheme cytochrome c from Desulfovibrio desulfuricans ATCC 27774, which is otherwise unrelated in the peptide chain folding pattern. The two propionate side chains on both heme groups are hydrogen-bonded to each other, a structural characteristic that to date also has not been reported in any other heme protein. The propionates of one of the heme groups are pulled toward the interior of the molecule due to a salt bridge and a number of hydrogen bonds between the propionates and conserved residues. We propose a hypothetical but plausible model of the NapAB complex in which the four redox centers are positioned in a virtually linear configuration which spans a distance of nearly 40 A, suggesting an efficient pathway for the transfer of electrons from NapC, the physiological electron donor of NapB, to a nitrate molecule at the catalytic site of NapA.

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  • The crystal structure of recombinant Haemophilus influenza NapB shows that the two heme molecules are stacked parallel and hydrogen bonded to each other via propionic acid side chains.

    “The crystal structure of the recombinant Haemophilus influenza NapB has revealed that the two heme molecules are stacked parallel and hydrogen bonded to each other via propionic acid side chains.251”

    From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [251]

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Authors
Brigé, A., Leys, D., Meyer, T. E., Cusanovich, M. A., & Van Beeumen, J. J.
Affiliations
  • University of Arizona (US)
  • Laboratory of Protein Biochemistry and Protein Engineering, State University of Gent, Ledeganckstraat 35, B-9000 Gent, Belgium, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
ORCID
Leys, David
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
2002-03-22
Volume
41
Issue
15
Pages
4827-4836
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/bi012144b
OpenAlex
W2005630792
Cited by
47
References
20
Citations by year
2024: 2 · 2023: 1 · 2022: 3 · 2020: 1 · 2019: 3 · 2018: 4 · 2017: 1 · 2016: 1 · 2015: 2 · 2014: 4 · 2013: 1
FWCI
2.80
Type
journal article
Language
en
Open access
closed
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
  • Research Explorer (The University of Manchester) (publishedVersion)
Funders
National Institute of General Medical Sciences (GM-21277, R01GM021277)
Topics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Hemoglobin structure and function
Keywords
nitrate reductase, periplasmic nitrate reductase, salt bridges, electron transfer pathway, Haemophilus influenzae, crystal structure
MeSH terms
Binding Sites, Cytochrome c Group, Desulfovibrio, Heme, Hydrogen Bonding, Models, Molecular, Nitrate Reductases, Oxidation-Reduction, Propionates, Protein Conformation, Protein Folding, Crystallography, X-Ray, Catalytic Domain, Protein Subunits, Nitrate Reductase

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