5GYJ

Structure of catalytically active sortase from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into Substrate Recognition by Clostridium difficile Sortase.

Yin, J.C.Fei, C.H.Lo, Y.C.Hsiao, Y.Y.Chang, J.C.Nix, J.C.Chang, Y.Y.Yang, L.W.Huang, I.H.Wang, S.

(2016) Front Cell Infect Microbiol 6: 160-160

  • DOI: https://doi.org/10.3389/fcimb.2016.00160
  • Primary Citation of Related Structures:  
    5GYJ

  • PubMed Abstract: 

    Sortases function as cysteine transpeptidases that catalyze the covalent attachment of virulence-associated surface proteins into the cell wall peptidoglycan in Gram-positive bacteria. The substrate proteins targeted by sortase enzymes have a cell wall sorting signal (CWSS) located at the C-terminus. Up to date, it is still not well understood how sortases with structural resemblance among different classes and diverse species of bacteria achieve substrate specificity. In this study, we focus on elucidating the molecular basis for specific recognition of peptide substrate PPKTG by Clostridium difficile sortase B (Cd-SrtB). Combining structural studies, biochemical assays and molecular dynamics simulations, we have constructed a computational model of Cd-SrtB ΔN26 -PPKTG complex and have validated the model by site-directed mutagensis studies and fluorescence resonance energy transfer (FRET)-based assay. Furthermore, we have revealed that the fourth amino acid in the N-terminal direction from cleavage site of PPKTG forms specific interaction with Cd-SrtB and plays an essential role in configuring the peptide to allow more efficient substrate-specific cleavage by Cd-SrtB.


  • Organizational Affiliation

    Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University Tainan, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative peptidase C60B, sortase B221Clostridioides difficile 630Mutation(s): 0 
Gene Names: CD630_27180
UniProt
Find proteins for Q183F3 (Clostridioides difficile (strain 630))
Explore Q183F3 
Go to UniProtKB:  Q183F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ183F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.25α = 90
b = 121.25β = 90
c = 121.25γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwanMOST 104-2320-B-006-050

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description