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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

Source organism: Desulfovibrio desulfuricans
Biochemical function: 4 iron, 4 sulfur cluster binding
Biological process: nitrate assimilation
Cellular component: periplasmic space

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EC 1.9.6.1: Nitrate reductase (cytochrome)

Reaction catalysed:
2 ferrocytochrome + nitrate + 2 H(+) = 2 ferricytochrome + nitrite
Systematic name:
Ferrocytochrome:nitrate oxidoreductase
Alternative Name(s):
  • Benzyl viologen-nitrate reductase
  • Respiratory nitrate reductase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF01568
Domain description: Molydopterin dinucleotide binding domain
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of Pfam domain PF01568 (Molydopterin dinucleotide binding domain) in Periplasmic nitrate reductase. Showing 1 copy in chain A.

PF00384
Domain description: Molybdopterin oxidoreductase
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of Pfam domain PF00384 (Molybdopterin oxidoreductase) in Periplasmic nitrate reductase. Showing 1 copy in chain A.

PF04879
Domain description: Molybdopterin oxidoreductase Fe4S4 domain
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of Pfam domain PF04879 (Molybdopterin oxidoreductase Fe4S4 domain) in Periplasmic nitrate reductase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR006963
Domain description: Molybdopterin oxidoreductase, 4Fe-4S domain
Occurring in:
  1. Periplasmic nitrate reductase
IPR006657
Domain description: Molybdopterin dinucleotide-binding domain
Occurring in:
  1. Periplasmic nitrate reductase
IPR041957
Domain description: Nitrate reductase NapA-like, molybdopterin-binding domain
Occurring in:
  1. Periplasmic nitrate reductase
IPR009010
Domain description: Aspartate decarboxylase-like domain superfamily
Occurring in:
  1. Periplasmic nitrate reductase
IPR006656
Domain description: Molybdopterin oxidoreductase
Occurring in:
  1. Periplasmic nitrate reductase
IPR010051
Domain description: Periplasmic nitrate reductase, large subunit
Occurring in:
  1. Periplasmic nitrate reductase

Structure domains

CATH CATH domains
3.40.228.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Dimethylsulfoxide Reductase; domain 2
Homology: Dimethylsulfoxide Reductase, domain 2
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of CATH domain 3.40.228.10 (Dimethylsulfoxide Reductase; domain 2) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
3.40.50.740
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: Rossmann fold
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of CATH domain 3.40.50.740 (Rossmann fold) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
2.40.40.20
Class: Mainly Beta
Architecture: Beta Barrel
Topology: Barwin-like endoglucanases
Homology: Barwin-like endoglucanases
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of CATH domain 2.40.40.20 (Barwin-like endoglucanases) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
2.20.25.90
Class: Mainly Beta
Architecture: Single Sheet
Topology: N-terminal domain of TfIIb
Homology: ADC-like domains
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of CATH domain 2.20.25.90 (N-terminal domain of TfIIb) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
SCOP SCOP annotations
50696
Class: All beta proteins
Fold: Double psi beta-barrel
Superfamily: ADC-like
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of SCOP domain 50696 (Formate dehydrogenase/DMSO reductase, C-terminal domain) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
53707
Class: Alpha and beta proteins (a/b)
Fold: Formate dehydrogenase/DMSO reductase, domains 1-3
Superfamily: Formate dehydrogenase/DMSO reductase, domains 1-3
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 2v45 contains 1 copy of SCOP domain 53707 (Formate dehydrogenase/DMSO reductase, domains 1-3) in Periplasmic nitrate reductase. Showing 1 copy in chain A.

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