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PDBsum entry 3h8i

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3h8i
Jmol
Contents
Protein chains
356 a.a. *
Ligands
FAD ×2
S3H ×2
PO4 ×9
Waters ×171
* Residue conservation analysis
PDB id:
3h8i
Name: Oxidoreductase
Title: The first x-ray structure of a sulfide:quinone oxidoreductase: insights into sulfide oxidation mechanism
Structure: Nadh oxidase. Chain: a, b. Ec: 1.6.99.3
Source: Acidianus ambivalens. Desulfurolobus ambivalens. Organism_taxid: 2283
Resolution:
2.65Å     R-factor:   0.197     R-free:   0.225
Authors: J.A.Brito,F.L.Sousa,M.Stelter,T.M.Bandeiras,C.Vonrhein, M.Teixeira,M.M.Pereira,M.Archer
Key ref: J.A.Brito et al. (2009). Structural and functional insights into sulfide:quinone oxidoreductase. Biochemistry, 48, 5613-5622. PubMed id: 19438211 DOI: 10.1021/bi9003827
Date:
29-Apr-09     Release date:   02-Jun-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7ZAG8  (Q7ZAG8_ACIAM) -  NADH oxidase
Seq:
Struc:
409 a.a.
356 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.6.99.3  - Nadh dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADH + acceptor = NAD+ + reduced acceptor
NADH
Bound ligand (Het Group name = FAD)
matches with 76.00% similarity
+ acceptor
= NAD(+)
+ reduced acceptor
      Cofactor: Flavoprotein; Iron-sulfur
Flavoprotein
Iron-sulfur
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     nucleotide binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9003827 Biochemistry 48:5613-5622 (2009)
PubMed id: 19438211  
 
 
Structural and functional insights into sulfide:quinone oxidoreductase.
J.A.Brito, F.L.Sousa, M.Stelter, T.M.Bandeiras, C.Vonrhein, M.Teixeira, M.M.Pereira, M.Archer.
 
  ABSTRACT  
 
A sulfide:quinone oxidoreductase (SQR) was isolated from the membranes of the hyperthermoacidophilic archaeon Acidianus ambivalens, and its X-ray structure, the first reported for an SQR, was determined to 2.6 A resolution. This enzyme was functionally and structurally characterized and was shown to have two redox active sites: a covalently bound FAD and an adjacent pair of cysteine residues. Most interestingly, the X-ray structure revealed the presence of a chain of three sulfur atoms bridging those two cysteine residues. The possible implications of this observation in the catalytic mechanism for sulfide oxidation are discussed, and the role of SQR in the sulfur dependent bioenergetics of A. ambivalens, linked to oxygen reduction, is addressed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20419499 Y.B.Ma, Z.F.Zhang, M.Y.Shao, K.H.Kang, Z.Tan, and J.L.Li (2011).
Sulfide:quinone Oxidoreductase from Echiuran Worm Urechis unicinctus.
  Mar Biotechnol (NY), 13, 93.  
19769466 D.R.Linden, M.D.Levitt, G.Farrugia, and J.H.Szurszewski (2010).
Endogenous production of H2S in the gastrointestinal tract: still in search of a physiologic function.
  Antioxid Redox Signal, 12, 1135-1146.  
20077566 M.Marcia, U.Ermler, G.Peng, and H.Michel (2010).
A new structure-based classification of sulfide:quinone oxidoreductases.
  Proteins, 78, 1073-1083.  
19725515 J.R.Wallen, T.C.Mallett, W.Boles, D.Parsonage, C.M.Furdui, P.A.Karplus, and A.Claiborne (2009).
Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking.
  Biochemistry, 48, 9650-9667.
PDB codes: 3icr 3ics 3ict
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.