Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.27 kDa 
• Atom Count: 10,044 
• Modelled Residue Count: 1,228 
• Deposited Residue Count: 1,228 
• Unique protein chains: 1

 1MPY

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

• PDB DOI:  https://doi.org/10.2210/pdb1MPY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 1998-10-20 Released: 1999-05-18 
• Deposition Author(s): Kita, A., Kita, S., Fujisawa, I., Inaka, K., Ishida, T., Horiike, K., Nozaki, M., Miki, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

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 7: 25-34

• PubMed: 10368270 
• DOI: https://doi.org/10.1016/s0969-2126(99)80006-9
• Primary Citation of Related Structures:  
  1MPY


• 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-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.

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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 122: 201

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATECHOL 2,3-DIOXYGENASE	A, B, C, D	307	Pseudomonas putida	Mutation(s): 0  Gene Names: xylE EC: 1.13.11.2
UniProt
Find proteins for P06622 (Pseudomonas putida) Explore P06622  Go to UniProtKB:  P06622

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACN	F [auth A], H [auth B], J [auth C], L [auth D]	ACETONE C3 H6 O CSCPPACGZOOCGX-UHFFFAOYSA-N
FE2	E [auth A], G [auth B], I [auth C], K [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.280 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264	α = 90
b = 264	β = 90
c = 59.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
WEIS	data reduction
DENZO	data reduction
WEIS	data scaling
PROTEIN	data scaling
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-18 
Deposition Author(s): Kita, A., Kita, S., Fujisawa, I., Inaka, K., Ishida, T., Horiike, K., Nozaki, M., Miki, K.

Revision History  

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