8XYF | pdb_00008xyf

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

• PDB DOI: https://doi.org/10.2210/pdb8XYF/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Staphylococcus phage GRCS, Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-01-19 Released: 2025-01-01 
• Deposition Author(s): Padmanabhan, B., Gopinath, K., Harshitha, H.N.
• Funding Organization(s): Science and Engineering Research Board (SERB)

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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

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

• PubMed: 39660753 
• DOI: https://doi.org/10.1002/prot.26777
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.
Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, India.
University of Trans-Disciplinary Health Sciences and Technology, Bengaluru, India.
Department of Microbiology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.98 kDa 
• Atom Count: 2,862 
• Modeled Residue Count: 319 
• Deposited Residue Count: 325 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin	A	256	Staphylococcus phage GRCS	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold shock-like protein CspC	B	69	Escherichia coli K-12	Mutation(s): 0  Gene Names: cspC, msmB, b1823, JW1812
UniProt
Find proteins for P0A9Y6 (Escherichia coli (strain K12)) Explore P0A9Y6  Go to UniProtKB:  P0A9Y6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	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 = 82.1	α = 90
b = 58.004	β = 121.55
c = 75.928	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Padmanabhan, B., Gopinath, K., Harshitha, H.N.

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Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	CRG/2019/002603

Revision History  

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