2BIB

Crystal structure of the complete modular teichioic acid phosphorylcholine esterase Pce (CbpE) from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights Into Pneumococcal Pathogenesis from Crystal Structure of the Modular Teichoic Acid Phosphorylcholine Esterase Pce

Hermoso, J.A.Lagartera, L.Gonzalez, A.Stelter, M.Garcia, P.Martinez-Ripoll, M.Garcia, J.L.Menendez, M.

(2005) Nat.Struct.Mol.Biol. 12: 533

  • DOI: 10.1038/nsmb940

  • PubMed Abstract: 
  • Phosphorylcholine, a specific component of the pneumococcal cell wall, is crucial in pathogenesis. It directly binds to the human platelet-activating factor (PAF) receptor and acts as a docking station for the family of surface-located choline-bindin ...

    Phosphorylcholine, a specific component of the pneumococcal cell wall, is crucial in pathogenesis. It directly binds to the human platelet-activating factor (PAF) receptor and acts as a docking station for the family of surface-located choline-binding proteins (CBP). The first structure of a complete pneumococcal CBP, Pce (or CbpE), has been solved in complex with the reaction product and choline analogs. Pce has a novel modular structure, with a globular N-terminal module containing a binuclear Zn(2+) catalytic center, and an elongated choline-binding module. Residues involved in substrate binding and catalysis are described and modular configuration of the active center accounts for in vivo features of teichoic acid hydrolysis. The hydrolysis of PAF by Pce and its regulatory role in phosphorylcholine decoration of the bacterial surface provide new insights into the critical function of Pce in pneumococcal adherence and invasiveness.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TEICHOIC ACID PHOSPHORYLCHOLINE ESTERASE/ CHOLINE BINDING PROTEIN
A
547Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: lytD
Find proteins for Q8DQ62 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DQ62
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC
Query on PC

Download SDF File 
Download CCD File 
A
PHOSPHOCHOLINE
C5 H15 N O4 P
YHHSONZFOIEMCP-UHFFFAOYSA-O
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

Download SDF File 
Download CCD File 
A
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.490α = 90.00
b = 58.120β = 108.29
c = 68.650γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other