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Crystal Structure of the Mo,Cu-CO Dehydrogenase (CODH), n-butylisocyanide-bound state

Source organism: Afipia carboxidovorans OM5
Biochemical function: oxidoreductase activity
Biological process: not assigned
Cellular component: not assigned

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EC 1.2.5.3: Aerobic carbon monoxide dehydrogenase

Reaction catalysed:
CO + a quinone + H(2)O = CO(2) + a quinol
Systematic name:
Carbon-monoxide:quinone oxidoreductase
Alternative Name(s):
  • CoxSML (gene names)
  • MoCu-CODH
  • Molybdoenzyme carbon monoxide dehydrogenase

GO terms

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF03450
Domain description: CO dehydrogenase flavoprotein C-terminal domain
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF03450 (CO dehydrogenase flavoprotein C-terminal domain) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.

PF00941
Domain description: FAD binding domain in molybdopterin dehydrogenase
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF00941 (FAD binding domain in molybdopterin dehydrogenase) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.

PF20256
Domain description: Molybdopterin cofactor-binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF20256 (Molybdopterin cofactor-binding domain) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.

PF02738
Domain description: Molybdopterin cofactor-binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF02738 (Molybdopterin cofactor-binding domain) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.

PF01315
Domain description: Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF01315 (Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.

PF01799
Domain description: [2Fe-2S] binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF01799 ([2Fe-2S] binding domain) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.

PF00111
Domain description: 2Fe-2S iron-sulfur cluster binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of Pfam domain PF00111 (2Fe-2S iron-sulfur cluster binding domain) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001041
Domain description: 2Fe-2S ferredoxin-type iron-sulfur binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
IPR005107
Domain description: CO dehydrogenase flavoprotein, C-terminal
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR036683
Domain description: CO dehydrogenase flavoprotein, C-terminal domain superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR016169
Domain description: FAD-binding, type PCMH, subdomain 2
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR002346
Domain description: Molybdopterin dehydrogenase, FAD-binding
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR036318
Domain description: FAD-binding, type PCMH-like superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR016167
Domain description: FAD-binding, type PCMH, subdomain 1
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR016166
Domain description: FAD-binding domain, PCMH-type
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
IPR046867
Domain description: Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR008274
Domain description: Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR037165
Domain description: Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR000674
Domain description: Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR012780
Domain description: Carbon-monoxide dehydrogenase, large subunit
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR016208
Domain description: Aldehyde oxidase/xanthine dehydrogenase-like
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR036856
Domain description: Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
IPR036884
Domain description: [2Fe-2S]-binding domain superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
IPR002888
Domain description: [2Fe-2S]-binding
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
IPR036010
Domain description: 2Fe-2S ferredoxin-like superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
IPR012675
Domain description: Beta-grasp domain superfamily
Occurring in:
  1. Carbon monoxide dehydrogenase small chain

Structure domains

CATH CATH domains
3.30.365.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Aldehyde Oxidoreductase; domain 4
Homology: Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 8 copies of CATH domain 3.30.365.10 (Aldehyde Oxidoreductase; domain 4) in Carbon monoxide dehydrogenase large chain. Showing 4 copies in chain B.
3.30.390.50
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Enolase-like; domain 1
Homology: CO dehydrogenase flavoprotein, C-terminal domain
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 3.30.390.50 (Enolase-like; domain 1) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.
3.30.465.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homology: Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 3.30.465.10 (Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.
3.30.43.10
Class: Alpha Beta
Architecture: 2-Layer Sandwich
Topology: Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homology: Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 3.30.43.10 (Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.
3.90.1170.50
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Aldehyde Oxidoreductase; domain 3
Homology: Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 3.90.1170.50 (Aldehyde Oxidoreductase; domain 3) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.
1.10.150.120
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: DNA polymerase; domain 1
Homology: [2Fe-2S]-binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 1.10.150.120 (DNA polymerase; domain 1) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.
3.10.20.30
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: Ubiquitin-like (UB roll)
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of CATH domain 3.10.20.30 (Ubiquitin-like (UB roll)) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.
SCOP SCOP annotations
55448
Class: Alpha and beta proteins (a+b)
Fold: CO dehydrogenase flavoprotein C-domain-like
Superfamily: CO dehydrogenase flavoprotein C-terminal domain-like
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 55448 (CO dehydrogenase flavoprotein C-terminal domain-like) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.
56187
Class: Alpha and beta proteins (a+b)
Fold: FAD-binding/transporter-associated domain-like
Superfamily: FAD-binding/transporter-associated domain-like
Occurring in:
  1. Carbon monoxide dehydrogenase medium chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 56187 (CO dehydrogenase flavoprotein N-terminal domain-like) in Carbon monoxide dehydrogenase medium chain. Showing 1 copy in chain C.
56004
Class: Alpha and beta proteins (a+b)
Fold: Molybdenum cofactor-binding domain
Superfamily: Molybdenum cofactor-binding domain
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 56004 (Molybdenum cofactor-binding domain) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.
54666
Class: Alpha and beta proteins (a+b)
Fold: alpha/beta-Hammerhead
Superfamily: CO dehydrogenase molybdoprotein N-domain-like
Occurring in:
  1. Carbon monoxide dehydrogenase large chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 54666 (CO dehydrogenase molybdoprotein N-domain-like) in Carbon monoxide dehydrogenase large chain. Showing 1 copy in chain B.
47742
Class: All alpha proteins
Fold: CO dehydrogenase ISP C-domain like
Superfamily: CO dehydrogenase ISP C-domain like
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 47742 (CO dehydrogenase ISP C-domain like) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.
54312
Class: Alpha and beta proteins (a+b)
Fold: beta-Grasp (ubiquitin-like)
Superfamily: 2Fe-2S ferredoxin-like
Occurring in:
  1. Carbon monoxide dehydrogenase small chain
The deposited structure of PDB entry 1n62 contains 2 copies of SCOP domain 54312 (2Fe-2S ferredoxin domains from multidomain proteins) in Carbon monoxide dehydrogenase small chain. Showing 1 copy in chain A.

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