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Crystal structure of the apomolybdo-NarGHI

Source organism: Escherichia coli
Biochemical function: nitrate reductase (quinone) activity
Biological process: nitrate assimilation
Cellular component: NarGHI complex

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EC 1.7.5.1: Nitrate reductase (quinone)

Reaction catalysed:
Nitrate + a quinol = nitrite + a quinone + H(2)O
Systematic name:
Nitrite:quinone oxidoreductase
Alternative Name(s):
  • Dissimilatory nitrate reductase
  • NarA
  • NarGHI
  • NarZ
  • Nitrate reductase A
  • Nitrate reductase Z
  • Quinol-nitrate oxidoreductase
  • Quinol/nitrate oxidoreductase
  • Quinol:nitrate oxidoreductase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF02665
Domain description: Nitrate reductase gamma subunit
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
The deposited structure of PDB entry 1siw contains 1 copy of Pfam domain PF02665 (Nitrate reductase gamma subunit) in Respiratory nitrate reductase 1 gamma chain. Showing 1 copy in chain C.

PF14711
Domain description: Respiratory nitrate reductase beta C-terminal
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
The deposited structure of PDB entry 1siw contains 1 copy of Pfam domain PF14711 (Respiratory nitrate reductase beta C-terminal) in Respiratory nitrate reductase 1 beta chain. Showing 1 copy in chain B.

PF13247
Domain description: 4Fe-4S dicluster domain
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
The deposited structure of PDB entry 1siw contains 1 copy of Pfam domain PF13247 (4Fe-4S dicluster domain) in Respiratory nitrate reductase 1 beta chain. Showing 1 copy in chain B.

PF01568
Domain description: Molydopterin dinucleotide binding domain
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of Pfam domain PF01568 (Molydopterin dinucleotide binding domain) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.

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

PF14710
Domain description: Respiratory nitrate reductase alpha N-terminal
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of Pfam domain PF14710 (Respiratory nitrate reductase alpha N-terminal) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR017896
Domain description: 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
IPR006547
Domain description: Nitrate reductase, beta subunit
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
IPR006655
Domain description: Molybdopterin oxidoreductase, prokaryotic, conserved site
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR006963
Domain description: Molybdopterin oxidoreductase, 4Fe-4S domain
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR023234
Domain description: NarG-like domain
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
IPR036197
Domain description: NarG-like superfamily
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
IPR003816
Domain description: Nitrate reductase, gamma subunit
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
IPR038262
Domain description: Nitrate reductase beta, C-terminal domain superfamily
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
IPR029263
Domain description: Respiratory nitrate reductase beta, C-terminal
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
IPR037943
Domain description: Nitrate reductase alpha subunit-like, MopB domain
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR006657
Domain description: Molybdopterin dinucleotide-binding domain
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR009010
Domain description: Aspartate decarboxylase-like domain superfamily
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR006656
Domain description: Molybdopterin oxidoreductase
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR027467
Domain description: Molybdopterin oxidoreductase, molybdopterin cofactor binding site
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR028189
Domain description: Nitrate reductase, alpha subunit, N-terminal
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR044906
Domain description: Nitrate reductase, alpha subunit, N-terminal domain superfamily
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
IPR006468
Domain description: Nitrate reductase, alpha subunit
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain

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. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 3.40.50.740 (Rossmann fold) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.
3.30.70.20
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Alpha-Beta Plaits
Homology: Alpha-Beta Plaits
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 3.30.70.20 (Alpha-Beta Plaits) in Respiratory nitrate reductase 1 beta chain. Showing 1 copy in chain B.
3.30.30.200
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Defensin A-like
Homology: Defensin A-like
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 3.30.30.200 (Defensin A-like) in Respiratory nitrate reductase 1 alpha chain. 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. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 2.40.40.20 (Barwin-like endoglucanases) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.
1.20.1700.20
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: AF1104-like
Homology: AF1104-like
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 1.20.1700.20 (AF1104-like) in Respiratory nitrate reductase 1 alpha chain. 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. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 3.40.228.10 (Dimethylsulfoxide Reductase; domain 2) in Respiratory nitrate reductase 1 alpha chain. 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. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 2.20.25.90 (N-terminal domain of TfIIb) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.
1.20.950.20
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Fumarate Reductase Cytochrome B subunit
Homology: Transmembrane di-heme cytochromes, Chain C
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 1.20.950.20 (Fumarate Reductase Cytochrome B subunit) in Respiratory nitrate reductase 1 gamma chain. Showing 1 copy in chain C.
1.10.3650.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: nitrate reductase domain fold
Homology: nitrate reductase domain like
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 1.10.3650.10 (nitrate reductase domain fold) in Respiratory nitrate reductase 1 beta chain. Showing 1 copy in chain B.
6.10.250.300
Class: Special
Architecture: Helix non-globular
Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 6.10.250.300 (Single alpha-helices involved in coiled-coils or other helix-helix interfaces) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.
4.10.1200.10
Class: Few Secondary Structures
Architecture: Irregular
Topology: nitrate reductase tail
Homology: nitrate reductase tail
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of CATH domain 4.10.1200.10 (nitrate reductase tail) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.
SCOP SCOP annotations
103502
Class: Membrane and cell surface proteins and peptides
Fold: Heme-binding four-helical bundle
Superfamily: Respiratory nitrate reductase 1 gamma chain
Occurring in:
  1. Respiratory nitrate reductase 1 gamma chain
The deposited structure of PDB entry 1siw contains 1 copy of SCOP domain 103502 (Respiratory nitrate reductase 1 gamma chain) in Respiratory nitrate reductase 1 gamma chain. Showing 1 copy in chain C.
54884
Class: Alpha and beta proteins (a+b)
Fold: Ferredoxin-like
Superfamily: 4Fe-4S ferredoxins
Occurring in:
  1. Respiratory nitrate reductase 1 beta chain
The deposited structure of PDB entry 1siw contains 1 copy of SCOP domain 54884 (Ferredoxin domains from multidomain proteins) in Respiratory nitrate reductase 1 beta chain. Showing 1 copy in chain B.
50696
Class: All beta proteins
Fold: Double psi beta-barrel
Superfamily: ADC-like
Occurring in:
  1. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of SCOP domain 50696 (Formate dehydrogenase/DMSO reductase, C-terminal domain) in Respiratory nitrate reductase 1 alpha chain. 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. Respiratory nitrate reductase 1 alpha chain
The deposited structure of PDB entry 1siw contains 1 copy of SCOP domain 53707 (Formate dehydrogenase/DMSO reductase, domains 1-3) in Respiratory nitrate reductase 1 alpha chain. Showing 1 copy in chain A.

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