1BOU

THREE-DIMENSIONAL STRUCTURE OF LIGAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 

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This is version 1.3 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

  • DOI: https://doi.org/10.1016/s0969-2126(99)80122-1
  • Primary Citation of Related Structures:  
    1B4U, 1BOU

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4,5-DIOXYGENASE ALPHA CHAIN
A, C
139Sphingomonas paucimobilisMutation(s): 0 
EC: 1.13.11.8
UniProt
Find proteins for P22635 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Explore P22635 
Go to UniProtKB:  P22635
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22635
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
4,5-DIOXYGENASE BETA CHAIN
B, D
302Sphingomonas paucimobilisMutation(s): 0 
EC: 1.13.11.8
UniProt
Find proteins for P22636 (Sphingobium sp. (strain NBRC 103272 / SYK-6))
Explore P22636 
Go to UniProtKB:  P22636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22636
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.4α = 90
b = 66.5β = 92.5
c = 119.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other