2J8G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report



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: 10.1074/jbc.M704317200
  • Structures With Same Primary Citation

  • 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 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.


    Related Citations: 
    • Structural Basis for Selective Recognition of Pneumococcal Cell Wall by Modular Endolysin from Phage Cp-1
      Hermoso, J.A., Monterroso, B., Albert, A., Galan, B., Ahrazem, O., Garcia, P., Martinez-Ripoll, M., Garcia, J.L., Menendez, M.
      (2003) Structure 11: 1239
    • Crystallization and Preliminary X-Ray Diffraction Studies of the Complete Modular Endolysin from Cp- 1, a Phage Infecting Streptococcus Pneumoniae
      Monterroso, B., Albert, A., Martinez-Ripoll, M., Garcia, P., Garcia, J.L., Menendez, M., Hermoso, J.A.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1487

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYMEA339Streptococcus phage Cp1Mutation(s): 1 
Gene Names: CPL122
EC: 3.2.1.17
Find proteins for P15057 (Streptococcus phage Cp-1)
Explore P15057 
Go to UniProtKB:  P15057
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3 N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
DGL
Query on DGL

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A
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
ALA
Query on ALA

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A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.52α = 90
b = 97.39β = 90
c = 127.14γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-04-10
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary