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 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 R6Mutation(s): 0 
Gene Names: lytCspr1431
EC: 3.2.1.17
Find proteins for Q8DP07 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DP07
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MUB
Query on MUB

Download CCD File 
A
N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-MDMHTWEWSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GLN
Query on GLN

Download CCD File 
A
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
CHT
Query on CHT

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-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 
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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