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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nsmb.1817
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.


    Related Citations: 
    • Insights Into the Structure-Function Relationships of Pneumococcal Cell Wall Lysozymes, Lytc and Cpl- 1.
      Monterroso, B.,Saiz, J.L.,Garcia, P.,Garcia, J.L.,Menendez, M.
      (2008) J.Biol.Chem. 283: 28618
    • Unravelling the Structure of the Pneumococcal Autolytic Lysozyme.
      Monterroso, B.,Lopez-Zumel, C.,Garcia, J.L.,Saiz, J.L.,Garcia, P.,Campillo, N.E.,Menendez, M.
      (2005) Biochem.J. 391: 41
    • The Molecular Characterization of the First Autolytic Lysozyme of Streptococcus Pneumoniae Reveals Evolutionary Mobile Domains.
      Garcia, P.,Paz Gonzalez, M.,Garcia, E.,Garcia, J.L.,Lopez, R.
      (1999) Mol.Microbiol. 33: 128


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,4-BETA-N-ACETYLMURAMIDASE
A
468Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: lytC
EC: 3.2.1.17
Find proteins for Q8DP07 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DP07
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CHT
Query on CHT

Download SDF File 
Download CCD File 
A
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
 Ligand Interaction
MU2
Query on MU2

Download SDF File 
Download CCD File 
A
N-ACETYLMURAMYL-L-ALANYL-D-ISOGLUTAMINE
C19 H32 N4 O11
SNTUQIQTAZQYIG-PUFOHHGRSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.400α = 90.00
b = 66.870β = 105.77
c = 77.920γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-04-03
    Type: Database references, Derived calculations, Non-polymer description