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Oxidoreductase PDB id
1kv9
Jmol
Contents
Protein chain
664 a.a. *
Ligands
PQQ
HEM
EPE
ACN
GOL
Metals
_CA
Waters ×732
* Residue conservation analysis
PDB id:
1kv9
Name: Oxidoreductase
Title: Structure at 1.9 a resolution of a quinohemoprotein alcohol dehydrogenase from pseudomonas putida hk5
Structure: Type ii quinohemoprotein alcohol dehydrogenase. Chain: a. Ec: 1.1.99.-
Source: Pseudomonas putida. Organism_taxid: 303
Resolution:
1.90Å     R-factor:   0.154     R-free:   0.189
Authors: Z.-W.Chen,K.Matsushita,T.Yamashita,T.Fujii,H.Toyama,O.Adachi H.D.Bellamy,F.S.Mathews
Key ref:
Z.W.Chen et al. (2002). Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5. Structure, 10, 837-849. PubMed id: 12057198 DOI: 10.1016/S0969-2126(02)00774-8
Date:
25-Jan-02     Release date:   10-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8GR64  (Q8GR64_PSEPU) -  Quinohemoprotein alcohol dehydrogenase ADH IIB
Seq:
Struc: 		 
Seq:
Struc: 		690 a.a.
664 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     6 terms  

 

 
DOI no: 10.1016/S0969-2126(02)00774-8 Structure 10:837-849 (2002)
PubMed id: 12057198  
 
 
Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
Z.W.Chen, K.Matsushita, T.Yamashita, T.A.Fujii, H.Toyama, O.Adachi, H.D.Bellamy, F.S.Mathews.
 
  ABSTRACT  
 
The type II quinohemoprotein alcohol dehydrogenase of Pseudomonas putida is a periplasmic enzyme that oxidizes substrate alcohols to the aldehyde and transfers electrons first to pyrroloquinoline quinone (PQQ) and then to an internal heme group. The 1.9 A resolution crystal structure reveals that the enzyme contains a large N-terminal eight-stranded beta propeller domain (approximately 60 kDa) similar to methanol dehydrogenase and a small C-terminal c-type cytochrome domain (approximately 10 kDa) similar to the cytochrome subunit of p-cresol methylhydoxylase. The PQQ is bound near the axis of the propeller domain about 14 A from the heme. A molecule of acetone, the product of the oxidation of isopropanol present during crystallization, appears to be bound in the active site cavity.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereo Diagrams of the Cytochrome Domain, the Active Site Cavity, and the Putative Azurin Binding Site(A) Comparison of the cytochrome domain of ADH IIB (residues 577-664) with the cytochrome subunit of p-cresol methylhydroxylase (PCMH). The five peptide fragments of high structural homology, indicated by roman numerals, are in blue, and the intervening segments of low structural homology as well as the heme groups are in red for ADH IIB and in yellow for PCMH.(B) Active site cavity of ADH IIB shown with chicken wire representation and containing the reaction product, acetone. The PQQ and the 13 side chains, mostly hydrophobic, of the quinoprotein domain that surround and help form the cavity are labeled.(C) Ca tracing of ADH IIB showing the active site cavity entrance and putative azurin binding site. The quinoprotein and cytochrome domains are green and azure, respectively, and the linker segment is violet. The residues lining the cavity (403-406 and 424-435) are blue, and the residues partially surrounding the putative azurin binding site (605-631) plus the heme are red. The cavity is represented as chicken wire, and the side chains separating the cavity from solvent, Phe378 and Phe425, as well as PQQ are also in blue.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 837-849) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21356200 J.Li, J.H.Gan, F.S.Mathews, and Z.X.Xia (2011).
The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase.
  Biochem Biophys Res Commun, 406, 621-626.  
19224199 B.Mennenga, C.W.Kay, and H.Görisch (2009).
Quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: the unusual disulfide ring formed by adjacent cysteine residues is essential for efficient electron transfer to cytochrome c550.
  Arch Microbiol, 191, 361-367.  
19202108 W.Promden, A.S.Vangnai, H.Toyama, K.Matsushita, and P.Pongsawasdi (2009).
Analysis of the promoter activities of the genes encoding three quinoprotein alcohol dehydrogenases in Pseudomonas putida HK5.
  Microbiology, 155, 594-603.  
17712582 M.J.Ellis, J.G.Grossmann, R.R.Eady, and S.S.Hasnain (2007).
Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases.
  J Biol Inorg Chem, 12, 1119-1127.  
16267040 C.W.Kay, B.Mennenga, H.Görisch, and R.Bittl (2006).
Structure of the pyrroloquinoline quinone radical in quinoprotein ethanol dehydrogenase.
  J Biol Chem, 281, 1470-1476.  
15608378 P.A.Williams, L.Coates, F.Mohammed, R.Gill, P.T.Erskine, A.Coker, S.P.Wood, C.Anthony, and J.B.Cooper (2005).
The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens.
  Acta Crystallogr D Biol Crystallogr, 61, 75-79.
PDB code: 1w6s
14997549 I.Hudáky, Z.Gáspári, O.Carugo, M.Cemazar, S.Pongor, and A.Perczel (2004).
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations.
  Proteins, 55, 152-168.  
14612441 M.D.Elias, S.Nakamura, C.T.Migita, H.Miyoshi, H.Toyama, K.Matsushita, O.Adachi, and M.Yamada (2004).
Occurrence of a bound ubiquinone and its function in Escherichia coli membrane-bound quinoprotein glucose dehydrogenase.
  J Biol Chem, 279, 3078-3083.  
15273299 S.Y.Reddy, and T.C.Bruice (2004).
Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase.
  Protein Sci, 13, 1965-1978.  
12843671 H.Toyama, T.Fujii, N.Aoki, K.Matsushita, and O.Adachi (2003).
Molecular cloning of quinohemoprotein alcohol dehydrogenase, ADH IIB, from Pseudomonas putida HK5.
  Biosci Biotechnol Biochem, 67, 1397-1400.  
  12547421 V.Anantharaman, L.Aravind, and E.V.Koonin (2003).
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
  Curr Opin Chem Biol, 7, 12-20.  
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 code is shown on the right.