7RD0

Crystal structure of C. difficile penicillin-binding protein 3 in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile.

Sacco, M.D.Wang, S.Adapa, S.R.Zhang, X.Lewandowski, E.M.Gongora, M.V.Keramisanou, D.Atlas, Z.D.Townsend, J.A.Gatdula, J.R.Morgan, R.T.Hammond, L.R.Marty, M.T.Wang, J.Eswara, P.J.Gelis, I.Jiang, R.H.Y.Sun, X.Chen, Y.

(2022) Nat Commun 13: 4370-4370

  • DOI: https://doi.org/10.1038/s41467-022-32086-6
  • Primary Citation of Related Structures:  
    7RCW, 7RCX, 7RCY, 7RCZ, 7RD0

  • PubMed Abstract: 

    Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn 2+ -binding motif that influences β-lactam binding and protein stability. The Zn 2+ -binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn 2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.


  • Organizational Affiliation

    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein513Clostridioides difficile R20291Mutation(s): 0 
Gene Names: CDR20291_1067
EC: 2.4.1.129
UniProt
Find proteins for Q18B92 (Clostridioides difficile (strain 630))
Explore Q18B92 
Go to UniProtKB:  Q18B92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18B92
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.02α = 90
b = 114.22β = 90
c = 154.63γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MoRDaphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI161762
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133617
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128624
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008804

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description