2BUQ

Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 in Complex with Catechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Biophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase

Brown, C.K.Vetting, M.W.Earhart, C.A.Ohlendorf, D.H.

(2004) Annu Rev Microbiol 58: 555-585

  • DOI: 10.1146/annurev.micro.57.030502.090927
  • Primary Citation of Related Structures:  
    2BUV, 2BUT, 2BUR, 2BUQ, 2BUM

  • PubMed 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 ...

    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.


    Related Citations: 
    • Crystallographic Studies of Intradiol Dioxygenases
      Vetting, M.
      (2001) Ph D Thesis --: --

    Organizational Affiliation

    Center for Metals in Biocatalysis and Department of Biochemistry, Molecular Biology, and Biophysics , Minneapolis, Minnesota 55455, USA. brow0927@umn.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAINA209Acinetobacter baylyi ADP1Mutation(s): 0 
Gene Names: pcaGACIAD1712
EC: 1.13.11.3
UniProt
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore P20371 
Go to UniProtKB:  P20371
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAINB241Acinetobacter baylyi ADP1Mutation(s): 0 
Gene Names: pcaHACIAD1711
EC: 1.13.11.3
UniProt
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore P20372 
Go to UniProtKB:  P20372
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAQ
Query on CAQ

Download Ideal Coordinates CCD File 
D [auth B], E [auth B]CATECHOL
C6 H6 O2
YCIMNLLNPGFGHC-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.7α = 90
b = 144.7β = 90
c = 144.7γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description