1GVM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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

  • DOI: https://doi.org/10.1016/s0022-2836(02)00596-x
  • Primary Citation of Related Structures:  
    1GVM

  • 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. 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AUTOLYSIN
A, B, C, D, E
A, B, C, D, E, F
136Streptococcus pneumoniaeMutation(s): 1 
EC: 3.5.1.28
UniProt
Find proteins for P06653 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P06653 
Go to UniProtKB:  P06653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06653
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DDQ
Query on DDQ

Download Ideal Coordinates CCD File 
AA [auth F]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
BA [auth F]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CHT
Query on CHT

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth E],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.717α = 90
b = 85.39β = 96.54
c = 204.136γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description