2WWD

3D-structure of the modular autolysin LytC from Streptococcus pneumoniae in complex with pneummococcal peptidoglycan fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Insights Into Pneumococcal Fratricide from the Crystal Structures of the Modular Killing Factor Lytc.

Perez-Dorado, I.Gonzalez, A.Morales, M.Sanles, R.Striker, W.Vollmer, W.Mobashery, S.Garcia, J.L.Martinez-Ripoll, M.Garcia, P.Hermoso, J.A.

(2010) Nat Struct Mol Biol 17: 576

  • DOI: https://doi.org/10.1038/nsmb.1817
  • Primary Citation of Related Structures:  
    2WW5, 2WWC, 2WWD

  • PubMed Abstract: 

    The first structure of a pneumococcal autolysin, that of the LytC lysozyme, has been solved in ternary complex with choline and a pneumococcal peptidoglycan (PG) fragment. The active site of the hydrolase module is not fully exposed but is oriented toward the choline-binding module, which accounts for its unique in vivo features in PG hydrolysis, its activation and its regulatory mechanisms. Because of the unusual hook-shaped conformation of the multimodular protein, it is only able to hydrolyze non-cross-linked PG chains, an assertion validated by additional experiments. These results explain the activation of LytC by choline-binding protein D (CbpD) in fratricide, a competence-programmed mechanism of predation of noncompetent sister cells. The results provide the first structural insights to our knowledge into the critical and central function that LytC plays in pneumococcal virulence and explain a long-standing puzzle of how murein hydrolases can be controlled to avoid self-lysis during bacterial growth and division.


  • Organizational Affiliation

    Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1,4-BETA-N-ACETYLMURAMIDASE468Streptococcus pneumoniae R6Mutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for Q8DP07 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DP07 
Go to UniProtKB:  Q8DP07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DP07
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download Ideal Coordinates CCD File 
R [auth A]GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
CHT
Query on CHT

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA
Query on ALA

Download Ideal Coordinates CCD File 
Q [auth A]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.4α = 90
b = 66.87β = 105.77
c = 77.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-04-03
    Changes: Database references, Derived calculations, Non-polymer description
  • 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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary