Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase from Escherichia coli
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The Escherichia coli NapA (periplasmic nitrate reductase) contains a [4Fe-4S] cluster and a Mo-bis-molybdopterin guanine dinucleotide cofactor. The NapA holoenzyme associates with a di-heme c-type cytochrome redox partner (NapB). These proteins have been purified and studied by spectropotentiometry, and the structure of NapA has been determined. In contrast to the well characterized heterodimeric NapAB systems ofalpha-proteobacteria, such as Rhodobacter sphaeroides and Paracoccus pantotrophus, the gamma-proteobacterial E. coli NapA and NapB proteins purify independently and not as a tight heterodimeric complex. This relatively weak interaction is reflected in dissociation constants of 15 and 32 mum determined for oxidized and reduced NapAB complexes, respectively. The surface electrostatic potential of E. coli NapA in the apparent NapB binding region is markedly less polar and anionic than that of the alpha-proteobacterial NapA, which may underlie the weaker binding of NapB. The molybdenum ion coordination sphere of E. coli NapA includes two molybdopterin guanine dinucleotide dithiolenes, a protein-derived cysteinyl ligand and an oxygen atom. The Mo-O bond length is 2.6 A, which is indicative of a water ligand. The potential range over which the Mo(6+) state is reduced to the Mo(5+) state in either NapA (between +100 and -100 mV) or the NapAB complex (-150 to -350 mV) is much lower than that reported for R. sphaeroides NapA (midpoint potential Mo(6+/5+) > +350 mV), and the form of the Mo(5+) EPR signal is quite distinct. In E. coli NapA or NapAB, the Mo(5+) state could not be further reduced to Mo(4+). We then propose a catalytic cycle for E. coli NapA in which nitrate binds to the Mo(5+) ion and where a stable des-oxo Mo(6+) species may participate.
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When nitrate reduction is coupled to formate oxidation, a proton gradient is generated across the cell membrane.
“In reality, when nitrate reduction is coupled to formate oxidation, a proton gradient is indeed generated across the cell membrane.”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [96]
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 [96]
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 [96]
The two larger inserts in Epsilonproteobacteria NapA expand upon the same polypeptide inserts observed in heterodimeric NapA like R. sphaeroides and E. coli.
“the two larger inserts in the Epsilonproteobacteria NapA expand upon the same polypeptide inserts observed in heterodimeric NapA like R. sphaeroides and E. coli (Fig. 8).96”
From Nitrate and periplasmic nitrate reductases (2014) · cites this paper as [96]
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 [96]
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- Authors
- 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.
- Affiliations
- University of East Anglia (GB)
- University of Birmingham (GB)
- Newcastle University (GB)
- Corresponding author
- Hemmings, Andrew M.
- Richardson, David J.
- ORCID
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2007-03
- Volume
- 282
- Issue
- 9
- Pages
- 6425-6437
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2044608755
- Cited by
- 120
- References
- 56
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 9 · 2023: 4 · 2022: 3 · 2021: 6 · 2020: 5 · 2019: 4 · 2018: 5 · 2017: 1 · 2016: 6 · 2015: 6 · 2014: 5 · 2013: 13 · 2012: 6
- FWCI
- 5.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- European Commission
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (B18695)
- 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 › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
- Keywords
- periplasmic nitrate reductase, napA, Escherichia coli, [4Fe-4S] cluster, cytochrome c550, protein-protein interaction, dissociation constant, surface electrostatic potential, molybdenum coordination, electron spin resonance
- MeSH terms
- Electrochemistry, Electron Spin Resonance Spectroscopy, Molybdenum, Oxidation-Reduction, Protein Binding, Crystallography, X-Ray, Escherichia coli Proteins, Nitrate Reductase, Static Electricity
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