3KMH

Crystal Structure of a Novel Sugar Isomerase from E. coli O157:H7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7.

van Staalduinen, L.M.Park, C.S.Yeom, S.J.Adams-Cioaba, M.A.Oh, D.K.Jia, Z.

(2010) J Mol Biol 401: 866-881

  • DOI: 10.1016/j.jmb.2010.06.063
  • Primary Citation of Related Structures:  
    3KMH, 3MPB

  • PubMed Abstract: 
  • Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a "hypothetical" protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known ...

    Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a "hypothetical" protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 A resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary-structure matching. Extensive substrate screening revealed that EcSI is capable of acting on d-lyxose and d-mannose. The complex structure of EcSI with fructose allowed the identification of key active-site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a nonpathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L3N6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-lyxose isomeraseA, B246Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ECs5070Z5688ECs_5070
EC: 5.3.1.15
UniProt
Find proteins for Q8X5Q7 (Escherichia coli O157:H7)
Explore Q8X5Q7 
Go to UniProtKB:  Q8X5Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X5Q7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPH
Query on IPH

Download Ideal Coordinates CCD File 
F [auth B]PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.35α = 90
b = 75.315β = 106.29
c = 61.778γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL2Mapmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description