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Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

Source organism: Cereibacter sphaeroides
Biochemical function: metal ion binding
Biological process: anaerobic respiration
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)
PF03892
Domain description: Nitrate reductase cytochrome c-type subunit (NapB)
Occurring in:
  1. Periplasmic nitrate reductase, electron transfer subunit
The deposited structure of PDB entry 1ogy contains 8 copies of Pfam domain PF03892 (Nitrate reductase cytochrome c-type subunit (NapB)) in Periplasmic nitrate reductase, electron transfer subunit. Showing 1 copy in chain B.

PF01568
Domain description: Molydopterin dinucleotide binding domain
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 1ogy contains 8 copies 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 1ogy contains 8 copies 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 1ogy contains 8 copies of Pfam domain PF04879 (Molybdopterin oxidoreductase Fe4S4 domain) in Periplasmic nitrate reductase. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR005591
Domain description: Nitrate reductase cytochrome c-type subunit NapB
Occurring in:
  1. Periplasmic nitrate reductase, electron transfer subunit
IPR006963
Domain description: Molybdopterin oxidoreductase, 4Fe-4S domain
Occurring in:
  1. Periplasmic nitrate reductase
IPR010051
Domain description: Periplasmic nitrate reductase, large subunit
Occurring in:
  1. Periplasmic nitrate reductase
IPR036280
Domain description: Multiheme cytochrome superfamily
Occurring in:
  1. Periplasmic nitrate reductase, electron transfer subunit
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
IPR027467
Domain description: Molybdopterin oxidoreductase, molybdopterin cofactor binding site
Occurring in:
  1. Periplasmic nitrate reductase

Structure domains

CATH CATH domains
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 1ogy contains 8 copies of CATH domain 3.40.50.740 (Rossmann fold) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
3.30.200.210
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Phosphorylase Kinase; domain 1
Homology: Phosphorylase Kinase; domain 1
Occurring in:
  1. Periplasmic nitrate reductase
The deposited structure of PDB entry 1ogy contains 8 copies of CATH domain 3.30.200.210 (Phosphorylase Kinase; domain 1) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
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 1ogy contains 8 copies of CATH domain 3.40.228.10 (Dimethylsulfoxide Reductase; domain 2) 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 1ogy contains 8 copies of CATH domain 2.40.40.20 (Barwin-like endoglucanases) in Periplasmic nitrate reductase. Showing 1 copy in chain A.
SCOP SCOP annotations
48711
Class: All alpha proteins
Fold: Multiheme cytochromes
Superfamily: Multiheme cytochromes
Occurring in:
  1. Periplasmic nitrate reductase, electron transfer subunit
The deposited structure of PDB entry 1ogy contains 8 copies of SCOP domain 48711 (Di-heme elbow motif) in Periplasmic nitrate reductase, electron transfer subunit. Showing 1 copy in chain B.
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 1ogy contains 8 copies 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 1ogy contains 8 copies 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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