PDBsum entry 1eir

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Oxidoreductase PDB id
Jmol PyMol
Protein chain
289 a.a. *
Waters ×145
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: 2,3-dihydroxybiphenyl-1,2-dioxygenase
Structure: 2,3-dihydroxybiphenyl-1,2-dioxygenase. Chain: a. Synonym: biphenyl-2,3-diol 1,2-dioxygenase, 23ohbp oxygenas engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 307. Strain: kks102. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
2.00Å     R-factor:   0.181     R-free:   0.231
Authors: T.Senda
Key ref: Y.Uragami et al. (2001). Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase. J Inorg Biochem, 83, 269-279. PubMed id: 11293547 DOI: 10.1016/S0162-0134(00)00172-0
28-Feb-00     Release date:   28-Feb-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P17297  (BPHC_PSES1) -  Biphenyl-2,3-diol 1,2-dioxygenase
293 a.a.
289 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Biphenyl-2,3-diol 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Bound ligand (Het Group name = BPY)
corresponds exactly
+ O(2)
= 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
      Cofactor: Mn(2+) or Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  


DOI no: 10.1016/S0162-0134(00)00172-0 J Inorg Biochem 83:269-279 (2001)
PubMed id: 11293547  
Crystal structures of substrate free and complex forms of reactivated BphC, an extradiol type ring-cleavage dioxygenase.
Y.Uragami, T.Senda, K.Sugimoto, N.Sato, V.Nagarajan, E.Masai, M.Fukuda, Y.Mitsu.
BphC derived from Pseudomonas sp. strain KKS102, an extradiol type catecholic dioxygenase, is a non-heam iron-containing enzyme, playing an important role in the degradation of biphenyl/PCB (Poly Chlorinated Biphenyls) in the microbe. Although we had earlier solved the crystal structure of KKS102 BphC, it was the inactive form with Fe(III) in the active site. In order to determine the active form structure, BphC was re-activated by anaerobic incubation with Fe(II) and ascorbate, and crystallized anaerobically. The crystal structures of activated BphC and its substrate complex (E x S complex) were determined at 2.0 A resolution under cryogenic condition. In addition, crystal structures of unactivated BphC in substrate free and complex forms were also re-determined. Comparison of activated and unactivated E x S complexes reveals that the orientation of the bound substrate in the active site is significantly different between the two. The structural comparison of the substrate free and complex forms of activated BphC show certain small conformational shifts around the active site upon substrate binding. As a result of the conformational shifts, His194, which has been suggested as the catalytic base, takes part in a weak hydrogen bond with hydroxyl group of the substrate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153851 A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, and L.Que (2011).
A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase.
  J Biol Inorg Chem, 16, 341-355.
PDB codes: 3ojj 3ojk 3ojn 3ojt
16217642 J.P.Emerson, M.L.Wagner, M.F.Reynolds, L.Que, M.J.Sadowsky, and L.P.Wackett (2005).
The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study.
  J Biol Inorg Chem, 10, 751-760.  
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
12039005 C.M.Wilmot, and A.R.Pearson (2002).
Cryocrystallography of metalloprotein reaction intermediates.
  Curr Opin Chem Biol, 6, 202-207.  
12415290 S.Dai, F.H.Vaillancourt, H.Maaroufi, N.M.Drouin, D.B.Neau, V.Snieckus, J.T.Bolin, and L.D.Eltis (2002).
Identification and analysis of a bottleneck in PCB biodegradation.
  Nat Struct Biol, 9, 934-939.
PDB codes: 1lgt 1lkd
11682193 C.H.Chua, Y.Feng, C.C.Yeo, H.E.Khoo, and C.L.Poh (2001).
Identification of amino acid residues essential for catalytic activity of gentisate 1,2-dioxygenase from Pseudomonas alcaligenes NCIB 9867.
  FEMS Microbiol Lett, 204, 141-146.  
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.