5I8L | pdb_00005i8l

Crystal structure of the full-length cell wall-binding module of Cpl7 mutant R223A

• PDB DOI: https://doi.org/10.2210/pdb5I8L/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus phage CP-7
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2016-02-19 Released: 2017-03-08 
• Deposition Author(s): Bernardo-Garcia, N., Silva-Martin, N., Uson, I., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.289 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan.

Bustamante, N., Iglesias-Bexiga, M., Bernardo-Garcia, N., Silva-Martin, N., Garcia, G., Campanero-Rhodes, M.A., Garcia, E., Uson, I., Buey, R.M., Garcia, P., Hermoso, J.A., Bruix, M., Menendez, M.

(2017) Sci Rep 7: 16494-16494

• PubMed: 29184076 
• DOI: https://doi.org/10.1038/s41598-017-16392-4
• Primary Citation Related Structures: 
  4CVD, 5I8L


• PubMed Abstract: 
  

  Endolysins, the cell wall lytic enzymes encoded by bacteriophages to release the phage progeny, are among the top alternatives to fight against multiresistant pathogenic bacteria; one of the current biggest challenges to global health. Their narrow range of susceptible bacteria relies, primarily, on targeting specific cell-wall receptors through specialized modules. The cell wall-binding domain of Cpl-7 endolysin, made of three CW_7 repeats, accounts for its extended-range of substrates. Using as model system the cell wall-binding domain of Cpl-7, here we describe the molecular basis for the bacterial cell wall recognition by the CW_7 motif, which is widely represented in sequences of cell wall hydrolases. We report the crystal and solution structure of the full-length domain, identify N-acetyl-D-glucosaminyl-(β1,4)-N-acetylmuramyl-L-alanyl-D-isoglutamine (GMDP) as the peptidoglycan (PG) target recognized by the CW_7 motifs, and characterize feasible GMDP-CW_7 contacts. Our data suggest that Cpl-7 cell wall-binding domain might simultaneously bind to three PG chains, and also highlight the potential use of CW_7-containing lysins as novel anti-infectives.

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Organizational Affiliation: 
• Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain.
CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.
Instituto de Biología Molecular de Barcelona, CSIC, Baldiri Reixach 13, 08028, Barcelona, Spain.
ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain.
Metabolic Engineering Group. Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Serrano 119, 28006, Madrid, Spain. [e-mail].
CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.71 kDa 
• Atom Count: 1,097 
• Modeled Residue Count: 143 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A	145	Streptococcus phage CP-7	Mutation(s): 3  Gene Names: CPL7 EC: 3.2.1.17
UniProt
Find proteins for P19385 (Streptococcus phage Cp-7) Explore P19385  Go to UniProtKB:  P19385

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.289 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.524	α = 90
b = 50.331	β = 90
c = 86.089	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Bernardo-Garcia, N., Silva-Martin, N., Uson, I., Hermoso, J.A.

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2017-12-20
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description