The crystal structure of SrfJ from salmonella typhimurium

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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Crystal Structure of the Salmonella Enterica Serovar Typhimurium Virulence Factor Srfj, a Glycoside Hydrolase Family Enzyme.

Kim, Y.-G.Kim, J.-H.Kim, K.-J.

(2009) J Bacteriol 191: 6550

  • DOI: https://doi.org/10.1128/JB.00641-09
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    To cause infection, Salmonella enterica serovar Typhimurium uses type III secretion systems, which are encoded on two Salmonella pathogenicity islands, SPI-1 and SPI-2, the latter of which is thought to play a crucial role in bacterial proliferation in Salmonella-containing vacuoles (SCVs) after invading cells. S. Typhimurium SrfJ, located outside SPI-2, is also known to be involved in Salmonella pathogenicity and has high amino acid sequence homology with human lysosomal glucosylceramidase (GlcCerase). We present the first crystal structure of SrfJ at a resolution of 1.8 A. The overall fold of SrfJ shares high structure similarities with that of human GlcCerase, comprising two distinctive domains: a (beta/alpha)(8)-barrel catalytic domain and a beta-sandwich domain. As in human GlcCerase, the pocket-shaped active site of SrfJ is located on the C-terminal side of the barrel, and two conserved glutamic acid residues are used for the enzyme catalysis. Moreover, a glycerol-bound form of SrfJ reveals that the glucose ring moiety of the substrate might similarly bind to the enzyme as to human GlcCerase, suggesting that SrfJ might function as a glycoside hydrolase. Although some structural differences are observed between SrfJ and human GlcCerase in the substrate entrance of the active site, we speculate that, based on the high structural similarities to human GlcCerase in the overall fold and the active-site environment, SrfJ might have a GlcCerase activity and use the activity to enhance Salmonella virulence by modifying SCV membrane lipids.

  • Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
447Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Find proteins for Q9KIJ7 (Salmonella typhimurium)
Explore Q9KIJ7 
Go to UniProtKB:  Q9KIJ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KIJ7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.6α = 90
b = 162.3β = 90
c = 169.6γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other