spacer
spacer

PDBsum entry 2buq

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2buq
Jmol
Contents
Protein chains
202 a.a. *
238 a.a. *
Ligands
CAQ ×2
Metals
_FE
Waters ×245
* Residue conservation analysis
PDB id:
2buq
Name: Oxidoreductase
Title: Crystal structure of wild-type protocatechuate 3,4- dioxygenase from acinetobacter sp. Adp1 in complex with catechol
Structure: Protocatechuate 3,4-dioxygenase alpha chain. Chain: a. Synonym: protocatechuate 3,4-dioxygenase, 3,4-pcd. Engineered: yes. Protocatechuate 3,4-dioxygenase beta chain. Chain: b. Synonym: protocatechuate 3,4-dioxygenase, 3,4-pcd. Engineered: yes
Source: Acinetobacter calcoaceticus. Organism_taxid: 62977. Strain: adp1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: 24mer (from PDB file)
Resolution:
1.8Å     R-factor:   0.165     R-free:   0.194
Authors: M.W.Vetting,M.P.Valley,D.A.D'Argenio,L.N.Ornston, J.D.Lipscomb,D.H.Ohlendorf
Key ref: C.K.Brown et al. (2004). Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1. Annu Rev Microbiol, 58, 555-585. PubMed id: 15487948
Date:
17-Jun-05     Release date:   05-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20371  (PCXA_ACIAD) -  Protocatechuate 3,4-dioxygenase alpha chain
Seq:
Struc:
209 a.a.
202 a.a.
Protein chain
Pfam   ArchSchema ?
P20372  (PCXB_ACIAD) -  Protocatechuate 3,4-dioxygenase beta chain
Seq:
Struc:
241 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.13.11.3  - Protocatechuate 3,4-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Benzoate Metabolism
      Reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate
3,4-dihydroxybenzoate
Bound ligand (Het Group name = CAQ)
matches with 72.00% similarity
+ O(2)
= 3-carboxy-cis,cis-muconate
      Cofactor: 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   5 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
Annu Rev Microbiol 58:555-585 (2004)
PubMed id: 15487948  
 
 
Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1.
C.K.Brown, M.W.Vetting, C.A.Earhart, D.H.Ohlendorf.
 
  ABSTRACT  
 
The catechol dioxygenases allow a wide variety of bacteria to use aromatic compounds as carbon sources by catalyzing the key ring-opening step. These enzymes use specifically either catechol or protocatechuate (2,3-dihydroxybenozate) as their substrates; they use a bare metal ion as the sole cofactor. To learn how this family of metalloenzymes functions, a structural analysis of designed and selected mutants of these enzymes has been undertaken. Here we review the results of this analysis on the nonheme ferric iron intradiol dioxygenase protocatechuate 3,4-dioxygenase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21221570 A.Gosling, S.J.Fowler, M.S.O'Shea, M.Straffon, G.Dumsday, and M.Zachariou (2011).
Metabolic production of a novel polymer feedstock, 3-carboxy muconate, from vanillin.
  Appl Microbiol Biotechnol, 90, 107-116.  
20081038 K.X.Zhao, Y.Huang, X.Chen, N.X.Wang, and S.J.Liu (2010).
PcaO positively regulates pcaHG of the beta-ketoadipate pathway in Corynebacterium glutamicum.
  J Bacteriol, 192, 1565-1572.  
20559823 M.Morikawa (2010).
Dioxygen activation responsible for oxidation of aliphatic and aromatic hydrocarbon compounds: current state and variants.
  Appl Microbiol Biotechnol, 87, 1595-1603.  
19845332 L.H.Do, and S.J.Lippard (2009).
2-Phenoxypyridyl dinucleating ligands for assembly of diiron(II) complexes: efficient reactivity with O(2) to form (mu-Oxo)diiron(III) units.
  Inorg Chem, 48, 10708-10719.  
17921203 C.E.Aitken, R.A.Marshall, and J.D.Puglisi (2008).
An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments.
  Biophys J, 94, 1826-1835.  
16153178 D.M.Young, D.Parke, and L.N.Ornston (2005).
Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation.
  Annu Rev Microbiol, 59, 519-551.  
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.