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PDBsum entry 3fc4

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protein ligands metals links
Oxidoreductase PDB id
3fc4
Jmol
Contents
Protein chain
907 a.a. *
Ligands
FES ×2
PCD
EDO ×3
Metals
_MG ×3
_CL ×3
Waters ×1183
* Residue conservation analysis
PDB id:
3fc4
Name: Oxidoreductase
Title: Ethylene glycol inhibited form of aldehyde oxidoreductase from desulfovibrio gigas
Structure: Aldehyde oxidoreductase. Chain: a. Synonym: molybdenum iron sulfur protein. Ec: 1.2.99.7
Source: Desulfovibrio gigas. Organism_taxid: 879
Resolution:
1.79Å     R-factor:   0.155     R-free:   0.189
Authors: T.Santos-Silva,M.J.Romao
Key ref: T.Santos-Silva et al. (2009). Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system. J Am Chem Soc, 131, 7990-7998. PubMed id: 19459677 DOI: 10.1021/ja809448r
Date:
21-Nov-08     Release date:   06-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q46509  (MOP_DESGI) -  Aldehyde oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
907 a.a.
907 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.2.99.7  - Aldehyde dehydrogenase (FAD-independent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + H2O + acceptor = a carboxylate + reduced acceptor
aldehyde
Bound ligand (Het Group name = EDO)
matches with 40.00% similarity
+ H(2)O
+ acceptor
= carboxylate
+ reduced acceptor
      Cofactor: Iron-sulfur; Molybdopterin cytosine dinucleotide
Iron-sulfur
Molybdopterin cytosine dinucleotide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/ja809448r J Am Chem Soc 131:7990-7998 (2009)
PubMed id: 19459677  
 
 
Kinetic, structural, and EPR studies reveal that aldehyde oxidoreductase from Desulfovibrio gigas does not need a sulfido ligand for catalysis and give evidence for a direct Mo-C interaction in a biological system.
T.Santos-Silva, F.Ferroni, A.Thapper, J.Marangon, P.J.González, A.C.Rizzi, I.Moura, J.J.Moura, M.J.Romão, C.D.Brondino.
 
  ABSTRACT  
 
Aldehyde oxidoreductase from Desulfovibrio gigas (DgAOR) is a member of the xanthine oxidase (XO) family of mononuclear Mo-enzymes that catalyzes the oxidation of aldehydes to carboxylic acids. The molybdenum site in the enzymes of the XO family shows a distorted square pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. We report here steady-state kinetic studies of DgAOR with the inhibitors cyanide, ethylene glycol, glycerol, and arsenite, together with crystallographic and EPR studies of the enzyme after reaction with the two alcohols. In contrast to what has been observed in other members of the XO family, cyanide, ethylene glycol, and glycerol are reversible inhibitors of DgAOR. Kinetic data with both cyanide and samples prepared from single crystals confirm that DgAOR does not need a sulfido ligand for catalysis and confirm the absence of this ligand in the coordination sphere of the molybdenum atom in the active enzyme. Addition of ethylene glycol and glycerol to dithionite-reduced DgAOR yields rhombic Mo(V) EPR signals, suggesting that the nearly square pyramidal coordination of the active enzyme is distorted upon alcohol inhibition. This is in agreement with the X-ray structure of the ethylene glycol and glycerol-inhibited enzyme, where the catalytically labile OH/OH(2) ligand is lost and both alcohols coordinate the Mo site in a eta(2) fashion. The two adducts present a direct interaction between the molybdenum and one of the carbon atoms of the alcohol moiety, which constitutes the first structural evidence for such a bond in a biological system.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21170563 L.B.Maia, and J.J.Moura (2011).
Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases.
  J Biol Inorg Chem, 16, 443-460.  
20645325 E.Cremades, J.Echeverría, and S.Alvarez (2010).
The trigonal prism in coordination chemistry.
  Chemistry, 16, 10380-10396.  
20095751 J.M.Dieterich, H.J.Werner, R.A.Mata, S.Metz, and W.Thiel (2010).
Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.
  J Chem Phys, 132, 035101.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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