1MPY

STRUCTURE OF CATECHOL 2,3-DIOXYGENASE (METAPYROCATECHASE) FROM PSEUDOMONAS PUTIDA MT-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.

Kita, A.Kita, S.Fujisawa, I.Inaka, K.Ishida, T.Horiike, K.Nozaki, M.Miki, K.

(1999) Structure Fold.Des. 7: 25-34


  • PubMed Abstract: 
  • Catechol dioxygenases catalyze the ring cleavage of catechol and its derivatives in either an intradiol or extradiol manner. These enzymes have a key role in the degradation of aromatic molecules in the environment by soil bacteria. Catechol 2, 3-dio ...

    Catechol dioxygenases catalyze the ring cleavage of catechol and its derivatives in either an intradiol or extradiol manner. These enzymes have a key role in the degradation of aromatic molecules in the environment by soil bacteria. Catechol 2, 3-dioxygenase catalyzes the incorporation of dioxygen into catechol and the extradiol ring cleavage to form 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase (metapyrocatechase, MPC) from Pseudomonas putida mt-2 was the first extradiol dioxygenase to be obtained in a pure form and has been studied extensively. The lack of an MPC structure has hampered the understanding of the general mechanism of extradiol dioxygenases.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of Expressed Pseudomonas Putida Catechol 2,3-Dioxygenase
      Kita, A.,Kita, S.,Inaka, K.,Ishida, T.,Horiike, K.,Nozaki, M.,Miki, K.
      (1997) J.Biochem.(Tokyo) 122: 201


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATECHOL 2,3-DIOXYGENASE
A, B, C, D
307Pseudomonas putidaGene Names: xylE
EC: 1.13.11.2
Find proteins for P06622 (Pseudomonas putida)
Go to UniProtKB:  P06622
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACN
Query on ACN

Download SDF File 
Download CCD File 
A, B, C, D
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, D
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.200 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 264.000α = 90.00
b = 264.000β = 90.00
c = 59.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
DENZOdata reduction
WEISdata scaling
WEISdata reduction
PROTEINdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance