1BOU

THREE-DIMENSIONAL STRUCTURE OF LIGAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.

Sugimoto, K.Senda, T.Aoshima, H.Masai, E.Fukuda, M.Mitsui, Y.

(1999) Structure 7: 953-965

  • Primary Citation of Related Structures:  1B4U

  • PubMed Abstract: 
  • Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III ext ...

    Sphingomonas paucimobilis SYK-6 utilizes an extradiol-type catecholic dioxygenase, the LigAB enzyme (a protocatechuate 4,5-dioxygenase), to oxidize protocatechuate (or 3,4-dihydroxybenzoic acid, PCA). The enzyme belongs to the family of class III extradiol-type catecholic dioxygenases catalyzing the ring-opening reaction of protocatechuate and related compounds. The primary structure of LigAB suggests that the enzyme has no evolutionary relationship with the family of class II extradiol-type catecholic dioxygenases. Both the class II and class III enzymes utilize a non-heme ferrous center for adding dioxygen to the substrate. By elucidating the structure of LigAB, we aimed to provide a structural basis for discussing the function of class III enzymes.


    Organizational Affiliation

    Department of BioEngineering, Nagaoka University of Technology, Niigata, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4,5-DIOXYGENASE ALPHA CHAIN
A, C
139Sphingomonas paucimobilisGene Names: ligA
EC: 1.13.11.8
Find proteins for P22635 (Sphingomonas paucimobilis)
Go to UniProtKB:  P22635
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
4,5-DIOXYGENASE BETA CHAIN
B, D
302Sphingomonas paucimobilisGene Names: ligB
EC: 1.13.11.8
Find proteins for P22636 (Sphingomonas paucimobilis)
Go to UniProtKB:  P22636
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.400α = 90.00
b = 66.500β = 92.50
c = 119.800γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
X-PLORrefinement
PROCESSdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance