2D40

Crystal Structure of Z3393 from Escherichia coli O157:H7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7

Adams, M.A.Singh, V.K.Keller, B.O.Jia, Z.

(2006) Mol Microbiol 61: 1469-1484

  • DOI: 10.1111/j.1365-2958.2006.05334.x
  • Primary Citation of Related Structures:  
    2D40

  • PubMed Abstract: 
  • Gentisic acid (2,5-dihydroxybenzoic acid) is a key intermediate in aerobic bacterial pathways that are responsible for the metabolism of a large number of aromatic compounds. The critical step of these pathways is the oxygen-dependent reaction catalysed by gentisate 1,2-dioxygenase which opens the aromatic ring of gentisate to form maleylpyruvate ...

    Gentisic acid (2,5-dihydroxybenzoic acid) is a key intermediate in aerobic bacterial pathways that are responsible for the metabolism of a large number of aromatic compounds. The critical step of these pathways is the oxygen-dependent reaction catalysed by gentisate 1,2-dioxygenase which opens the aromatic ring of gentisate to form maleylpyruvate. From gentisic acid, the cell derives carbon and energy through the conversion of maleylpyruvate to central metabolites. We have confirmed the annotation of a gentisate 1,2-dioygenase from the pathogenic O157:H7 Escherichia coli strain and present the first structural characterization of this family of enzymes. The identity of the reaction product was revealed using tandem mass spectroscopy. The operon responsible for the degradation of gentisate in this organism exhibits a high degree of conservation with the gentisate-degrading operons of other pathogenic bacteria, including the Shiga toxin-producing E. coli O103:H2, but does not appear to be present in non-pathogenic strains. The acquisition of the gentisate operon may represent a special adaptation to meet carbon source requirements under conditions of environmental stress and may provide a selective advantage for enterohaemorrhagic E. coli relative to their non-pathogenic counterparts.


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, ON, Canada K7L 3N6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative gentisate 1,2-dioxygenaseA, B, C, D354Escherichia coli O157:H7Mutation(s): 7 
Gene Names: 
EC: 1.13.11.4
UniProt
Find proteins for Q8X655 (Escherichia coli O157:H7)
Explore Q8X655 
Go to UniProtKB:  Q8X655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X655
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.134α = 114.08
b = 76.075β = 94.93
c = 85.464γ = 108.11
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description