1GVM

CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Two New Crystal Forms of the Choline-Binding Domain of the Major Pneumococcal Autolysin: Insights Into the Dynamics of the Active Dimeric

Fernandez-Tornero, C.Garcia, E.Lopez, R.Gimenez-Gallego, G.Romero, A.

(2002) J.Mol.Biol. 321: 163


  • PubMed Abstract: 
  • Very little is known about the in vivo regulation of the catalytic activity of the major pneumococcal autolysin (LytA), a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone ...

    Very little is known about the in vivo regulation of the catalytic activity of the major pneumococcal autolysin (LytA), a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. Two new crystal forms of the cell wall anchoring domain of LytA were obtained, and their structures were solved and refined to 2.4A and 2.8A resolution. The domain is a homodimer with a boomerang-like shape in which the tertiary structure of each monomer is comprised by six independent beta hairpins arranged in a superhelical fashion. Choline molecules at the hydrophobic interface of consecutive hairpins maintain this unique structure. The C-terminal hairpin (last 13 residues of LytA) in the solenoid is responsible for the formation of the catalytically active homodimer. Although the general fold in the structures derived from both crystal forms is essentially the same, two different conformations of the basic homodimer are observed. Biochemical approaches have demonstrated the fundamental role of the 11 C-terminal residues in the catalytic activity of LytA. The studies reported here reveal the importance of some amino acid residues at the C terminus in the determination of the relative distance of the active dimeric form of the autolysin, which appears to be essential for the catalytic activity of this enzyme.


    Related Citations: 
    • A Novel Solenoid Fold in the Cell Wall Anchoring Domain of the Pneumococcal Virulence Factorlyta
      Fernandez-Tornero, C.,Lopez, R.,Garcia, E.,Gimenez-Gallego, G.,Romero, A.
      (2001) Nat.Struct.Mol.Biol. 8: 1020


    Organizational Affiliation

    Departamento de Estructura y Función de Proteínas, Centro de Investigaciones Biológicas-CSIC, C/Velázquez 144, Madrid 28006, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AUTOLYSIN
A, B, C, D, E, F
136Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Gene Names: lytA
EC: 3.5.1.28
Find proteins for P06653 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P06653
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDQ
Query on DDQ

Download SDF File 
Download CCD File 
F
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
 Ligand Interaction
CHT
Query on CHT

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 56.717α = 90.00
b = 85.390β = 96.54
c = 204.136γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance