6KYD

Structure of the R217A mutant of Clostridium difficile sortase B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional analysis ofClostridium difficilesortase B reveals key residues for catalytic activity and substrate specificity.

Kang, C.Y.Huang, I.H.Chou, C.C.Wu, T.Y.Chang, J.C.Hsiao, Y.Y.Cheng, C.H.Tsai, W.J.Hsu, K.C.Wang, S.

(2020) J Biol Chem 295: 3734-3745

  • DOI: https://doi.org/10.1074/jbc.RA119.011322
  • Primary Citation of Related Structures:  
    6KYC, 6KYD

  • PubMed Abstract: 

    Most of Gram-positive bacteria anchor surface proteins to the peptidoglycan cell wall by sortase, a cysteine transpeptidase that targets proteins displaying a cell wall sorting signal. Unlike other bacteria, Clostridium difficile , the major human pathogen responsible for antibiotic-associated diarrhea, has only a single functional sortase (SrtB). Sortase's vital importance in bacterial virulence has been long recognized, and C. difficile sortase B (Cd-SrtB) has become an attractive therapeutic target for managing C. difficile infection. A better understanding of the molecular activity of Cd-SrtB may help spur the development of effective agents against C. difficile infection. In this study, using site-directed mutagenesis, biochemical and biophysical tools, LC-MS/MS, and crystallographic analyses, we identified key residues essential for Cd-SrtB catalysis and substrate recognition. To the best of our knowledge, we report the first evidence that a conserved serine residue near the active site participates in the catalytic activity of Cd-SrtB and also SrtB from Staphylococcus aureus The serine residue indispensable for SrtB activity may be involved in stabilizing a thioacyl-enzyme intermediate because it is neither a nucleophilic residue nor a substrate-interacting residue, based on the LC-MS/MS data and available structural models of SrtB-substrate complexes. Furthermore, we also demonstrated that residues 163-168 located on the β6/β7 loop of Cd-SrtB dominate specific recognition of the peptide substrate PPKTG. The results of this work reveal key residues with roles in catalysis and substrate specificity of Cd-SrtB.


  • Organizational Affiliation

    Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, 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): 1 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.895α = 90
b = 120.895β = 90
c = 120.895γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan108-2320-B-006-012-

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description