› 2v3v

X-ray diffraction
1.99Å resolution

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand

Released:
DOI: 10.2210/pdb2v3v/pdb
PDB entry 2v3v coloured by chain, front view.
PDB entry 2v3v coloured by chain, side view.
PDB entry 2v3v coloured by chain, top view.
Source organism: Desulfovibrio desulfuricans
Primary publication:
Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.
Najmudin S, González PJ, Trincão J, Coelho C, Mukhopadhyay A, Cerqueira NM, Romão CC, Moura I, Moura JJ, Brondino CD, Romão MJ
J Biol Inorg Chem 13 737-53 (2008)
PMID: 18327621

Function and Biology Details

Reaction catalysed: 
2 ferrocytochrome + nitrate + 2 H(+) = 2 ferricytochrome + nitrite
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160493 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Periplasmic nitrate reductase Chain: A
Molecule details ›
Chain: A
Length: 723 amino acids
Theoretical weight: 80.39 KDa
Source organism: Desulfovibrio desulfuricans
UniProt:
  • Canonical: P81186 (Residues: 33-755; Coverage: 100%)
Gene names: Ddes_0616, nap, napA
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand MGD 2 x MGD
4 bound ligands:
Ligand SF4 1 x SF4
Ligand MO 1 x MO
Ligand UNX 1 x UNX
Ligand LCP 4 x LCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P3121
Unit cell:
a: 106.566Å b: 106.566Å c: 135.479Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.182 0.246

Quick links

Citations

15 review citations

The mononuclear molybdenum enzymes.
Hille et al. (2014)
14 more

2 mentions without citation

Pyranopterin conformation defines the function of molybdenum and tungsten enzymes.
Rothery et al. (2012)
1 more