8XYF | pdb_00008xyf

Crystal structure of Holo-PlyGRCS, a bacteriophage Endolysin in complex with Cold shock protein C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

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 Basis for the Essential Role of Ca 2+ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin-Resistant Staphylococcus aureus.

Krishnappa, G.Nagaraj, H.SureshKumar, H.B.Mandal, M.Padavattan, S.Bahubali, V.H.Thiyagarajan, S.Padmanabhan, B.

(2025) Proteins 93: 920-933

  • DOI: https://doi.org/10.1002/prot.26777
  • Primary Citation of Related Structures:  
    8XYF

  • PubMed Abstract: 

    Staphylococcus aureus causes a wide range of infections, from mild skin conditions to severe, life-threatening diseases. Bacteriophage endolysins exhibit a selective capacity to degrade the peptidoglycan layer of Gram-positive bacteria, making promising biotherapeutic agents against antibiotic-resistant infections. PlyGRCS, a specific endolysin derived from S. aureus, comprises a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Ca 2+ ions are essential for the CHAP domain's catalytic function. The crystal structure of PlyGRCS, determined in the absence of Ca 2+ and refined to a resolution of 1.67 Å, revealed significant conformational changes in the Ca 2+ binding site. Antimicrobial assays with Ca 2+ -deficient PlyGRCS and mutants targeting key residues in the catalytic and Ca 2+ binding regions highlighted the importance of specific functional residues for lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). These structural and microbial studies provide valuable insights into the critical residues contributing to PlyGRCS's bacteriolytic efficacy against MRSA.


  • Organizational Affiliation

    Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin256Staphylococcus phage GRCSMutation(s): 0 
Gene Names: GRCS_0015
EC: 3.5.1.28
UniProt
Find proteins for W6EBY7 (Staphylococcus phage GRCS)
Explore W6EBY7 
Go to UniProtKB:  W6EBY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW6EBY7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cold shock-like protein CspC69Escherichia coli K-12Mutation(s): 0 
Gene Names: cspCmsmBb1823JW1812
UniProt
Find proteins for P0A9Y6 (Escherichia coli (strain K12))
Explore P0A9Y6 
Go to UniProtKB:  P0A9Y6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9Y6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.1α = 90
b = 58.004β = 121.55
c = 75.928γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaCRG/2019/002603

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references