1DMH

STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.

Vetting, M.W.Ohlendorf, D.H.

(2000) Structure Fold.Des. 8: 429-440

  • Primary Citation of Related Structures:  1DLM, 1DLQ, 1DLT

  • PubMed Abstract: 
  • Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalyti ...

    Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. Catechol 1,2-dioxygenases (1, 2-CTDs) have a rudimentary design structure - a homodimer with one catalytic non-heme ferric ion per monomer, that is (alphaFe(3+))(2). This is in contrast to the archetypical intradiol dioxygenase protocatechuate 3,4-dioxygenase (3,4-PCD), which forms more diverse oligomers, such as (alphabetaFe(3+))(2-12).


    Related Citations: 
    • DNA Sequence of the Acinetobacter calcoaceticus Catechol 1,2-dioxygenase I Structural Gene catA: Evidence for Evolutionary Divergence of Intradiol Dioxygenases by Aquisition of DNA Sequence Repetitions
      Neidle, E.L.,Harnett, C.,Bonitz, S.,Ornston, L.N.
      (1988) J.Bacteriol. 170: 4874
    • Structure of Protocatechuate 3,4-dioxygenase from Psuedomonas aeruginosa at 2.15 A Resolution
      Ohlendorf, D.H.,Orville, A.M.,Lipscomb, J.D.
      (1994) J.Mol.Biol. 244: 586
    • Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe+3 Ligand Displacement in Response to Substrate Binding.
      Orville, A.M.,Lipscomb, J.D.,Ohlendorf, D.H.
      (1997) Biochemistry 36: 10052


    Organizational Affiliation

    The department of Biochemistry, Molecular Biology and Biophysics, Center for Metals in Biocatalysis, University of Minnesota Medical School, Minneapolis, MN 55455-0347, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATECHOL 1,2-DIOXYGENASE
A, B
311Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)Gene Names: catA
EC: 1.13.11.1
Find proteins for P07773 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Go to UniProtKB:  P07773
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIO
Query on LIO

Download SDF File 
Download CCD File 
A, B
[1-PENTADECANOYL-2-DECANOYL-GLYCEROL-3-YL]PHOSPHONYL CHOLINE
C33 H67 N O8 P
YAOVLDDMIGILIT-WJOKGBTCSA-O
 Ligand Interaction
MCT
Query on MCT

Download SDF File 
Download CCD File 
A, B
4-METHYLCATECHOL
4-METHYL-1,2-BENZENEDIOL
C7 H8 O2
ZBCATMYQYDCTIZ-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.800α = 90.00
b = 88.000β = 96.30
c = 84.400γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
X-GENdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description