2IXV

Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

Starting Model: experimental
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This is version 3.1 of the entry. See complete history


Literature

Elucidation of the Molecular Recognition of Bacterial Cell Wall by Modular Pneumococcal Phage Endolysin Cpl-1.

Perez-Dorado, I.Campillo, N.E.Monterroso, B.Hesek, D.Lee, M.Paez, J.A.Garcia, P.Martinez-Ripoll, M.Garcia, J.L.Mobashery, S.Menendez, M.Hermoso, J.A.

(2007) J Biol Chem 282: 24990

  • DOI: https://doi.org/10.1074/jbc.M704317200
  • Primary Citation of Related Structures:  
    2IXU, 2IXV, 2J8F, 2J8G

  • PubMed Abstract: 

    Pneumococcal bacteriophage-encoded lysins are modular proteins that have been shown to act as enzymatic antimicrobial agents (enzybiotics) in treatment of streptococcal infections. The first x-ray crystal structures of the Cpl-1 lysin, encoded by the pneumococcal phage Cp-1, in complex with three bacterial cell wall peptidoglycan (PG) analogues are reported herein. The Cpl-1 structure is folded in two well defined modules, one responsible for anchoring to the pneumococcal cell wall and the other, a catalytic module, that hydrolyzes the PG. Conformational rearrangement of Tyr-127 is a critical event in molecular recognition of a stretch of five saccharide rings of the polymeric peptidoglycan (cell wall). The PG is bound at a stretch of the surface that is defined as the peptidoglycan-binding sites 1 and 2, the juncture of which catalysis takes place. The peptidoglycan-binding site 1 binds to a stretch of three saccharides of the peptidoglycan in a conformation essentially identical to that of the peptidoglycan in solution. In contrast, binding of two peptidoglycan saccharides at the peptidoglycan-binding site 2 introduces a kink into the solution structure of the peptidoglycan, en route to catalytic turnover. These findings provide the first structural evidence on recognition of the peptidoglycan and shed light on the discrete events of cell wall degradation by Cpl-1.


  • Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME339Streptococcus phage Cp1Mutation(s): 1 
EC: 3.2.1.17
UniProt
Find proteins for P15057 (Streptococcus phage Cp-1)
Explore P15057 
Go to UniProtKB:  P15057
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15057
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid
B
2N/A
Glycosylation Resources
GlyTouCan:  G88499BX
GlyCosmos:  G88499BX
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.965α = 90
b = 96.443β = 90
c = 127.073γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-10
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 2.0: 2020-07-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary