spacer

Overview for MACiE Entry M0107

Version history

General Information

EC Number: 1.2.99.2 (A member of the Oxidoreductases, Acting on the aldehyde or oxo group of donors, With other acceptors)

Enzyme Name: carbon-monoxide dehydrogenase (acceptor)

Biological Species: Oligotropha carboxidovorans (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P19919 - Carbon monoxide dehydrogenase large chain

Representative PDB Code: 1n62 - CRYSTAL STRUCTURE OF THE MO,CU-CO DEHYDROGENASE (CODH), N-BUTYLISOCYANIDE-BOUND STATE (Resolution = 1.09 Å).

Catalytic CATH Codes:

  • 3.30.365.10 - Aldehyde Oxidoreductase; domain 4
  • Unassigned Domain

"Other" CATH Codes:

  • 3.10.20.30 - Ubiquitin-like (UB roll)
  • 1.10.150.120 - DNA polymerase; domain 1
  • 3.30.465.10 - Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
  • 3.30.365.10 - Aldehyde Oxidoreductase; domain 4
  • 3.30.390.50 - Enolase-like; domain 1
  • 3.90.1170.50 - Aldehyde Oxidoreductase; domain 3
  • 3.30.43.10 - Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
  • Unassigned Domain

Display structure information

Overall Reaction:

Image of acceptor

Image of carbon monoxide

Image of water

right arrow

Image of proton

Image of carbon dioxide

Image of reduced acceptor

acceptor
C00028
CHEBI:15339
carbon monoxide
C00237
CHEBI:17245
water
C00001
CHEBI:15377
2 proton
C00080
CHEBI:24636
carbon dioxide
C00011
CHEBI:16526
reduced acceptor
C00030
CHEBI:17499

This reaction is irreversible.

Overall Comment: This enzyme uses many electron acceptors, these include ferredoxin, methyl viologen and benzyl viologen and flavins but not pyridine nucleotides.


View similar reactions


Stepwise Description of the Reaction

Step 1Carbon monoxide coordinates to the Cu(I) centre.
Step 2The Carbanion of carbon monoxide initiates a nucleophilic attack on the oxo group coordinated to the Mo(VI) centre, which results in the reduction of the molybdenum to Mo(IV). The C#O triple bond reduces in order to C=O.
Step 3The sulfur dianion bridging the Mo(IV) and Cu(I) centres initiates a nucleophilic attack on the carbocation in a substitution reaction that displaces the carbon from the Cu(I) centre.
Step 4The carbonyl oxygen initiates a nucleophilic attack on the Cu(I) centre in a substitution reaction that displaces the bridging sulfur ligand from the Cu(I) centre.
Step 5Water initiates a nucleophilic attack on the Mo(IV) centre, displacing the negatively charged oxygen of the carboxylate group in a substitution reaction, which initiates an elimination of the sulfur group, to reform the bridging sulfur dianion and the formation of carbon dioxide, which decoordinates from the metal centre.
Step 6Glu763 deprotonates water, initiating a single electron transfer from the Mo(IV) centre, through two iron-sulfur clusters to FAD, and thence to an external electron acceptor.
Step 7Water deprotonates Glu763, which then deprotonates the Mo(V) bound hydroxide, initiating the second single electron transfer, through two iron-sulfur clusters to FAD, and thence to an external electron acceptor. This regenerates the cofactor.
Step 8Water deprotonates Glu763 in an inferred return step.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Cys 388 B Side Chain
Glu 763 B Side Chain

Organic Cofactors for M0107

Type Identity Chain
FAD FAD 3932 Overview

Metal Cofactors for M0107

Type Het group Number Chain
iron FES 3907 x Overview
iron FES 3908 x Overview
copper CUB 3921 x Overview
molybdenum CUB 3921 x Overview

References

  1. H. Dobbek et al. (2002), Proc. Natl Acad. Sci. USA, 99, 15971-15976. Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution.
    Medline: 12475995
  2. M. Hofmann et al. (2005), J. Biol. Inorg. Chem., 10, 490-495. The mechanism of Mo-/Cu-dependent CO dehydrogenase.
    Medline: 15971074

Homologue information for M0107 (1n62)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0105 aldehyde oxidase
1.2.3.1
1vlb 3.30.365.10
3.10.20.30
1.10.150.120
3.90.1170.50
0.34540.5258Compare

Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

GOA logo
catalytic activity (molecular function)
copper ion binding (molecular function)
electron carrier activity (molecular function)
oxidoreductase activity (molecular function)
carbon-monoxide dehydrogenase (acceptor) activity (molecular function)
molybdenum ion binding (molecular function)
metal ion binding (molecular function)
flavin adenine dinucleotide binding (molecular function)
iron-sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
spacer
spacer