3C2X

Crystal structure of peptidoglycan recognition protein at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the peptidoglycan recognition protein at 1.8 A resolution reveals dual strategy to combat infection through two independent functional homodimers

Sharma, P.Singh, N.Sinha, M.Sharma, S.Perbandt, M.Betzel, C.Kaur, P.Srinivasan, A.Singh, T.P.

(2008) J.Mol.Biol. 378: 921-930

  • DOI: 10.1016/j.jmb.2008.03.018

  • PubMed Abstract: 
  • The mammalian peptidoglycan recognition protein-S (PGRP-S) binds to peptidoglycans (PGNs), which are essential components of the cell wall of bacteria. The protein was isolated from the samples of milk obtained from camels with mastitis and purified ...

    The mammalian peptidoglycan recognition protein-S (PGRP-S) binds to peptidoglycans (PGNs), which are essential components of the cell wall of bacteria. The protein was isolated from the samples of milk obtained from camels with mastitis and purified to homogeneity and crystallized. The crystals belong to orthorhombic space group I222 with a=87.0 A, b=101.7 A and c=162.3 A having four crystallographically independent molecules in the asymmetric unit. The structure has been determined using X-ray crystallographic data and refined to 1.8 A resolution. Overall, the structures of all the four crystallographically independent molecules are identical. The folding of PGRP-S consists of a central beta-sheet with five beta-strands, four parallel and one antiparallel, and three alpha-helices. This protein fold provides two functional sites. The first of these is the PGN-binding site, located on the groove that opens on the surface in the direction opposite to the location of the N terminus. The second site is implicated to be involved in the binding of non-PGN molecules, it also includes putative N-terminal segment residues (1-31) and helix alpha2 in the extended binding. The structure reveals a novel arrangement of PGRP-S molecules in which two pairs of molecules associate to form two independent dimers. The first dimer is formed by two molecules with N-terminal segments at the interface in which non-PGN binding sites are buried completely, whereas the PGN-binding sites of two participating molecules are fully exposed at the opposite ends of the dimer. In the second dimer, PGN-binding sites are buried at the interface while non-PGN binding sites are fully exposed at the opposite ends of the dimer. This form of dimeric arrangement is unique and seems to be aimed at enhancing the capability of the protein against specific invading bacteria. This mode of functional dimerization enhances efficiency and specificity, and is observed for the first time in the family of PGRP molecules.


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan recognition protein
A, B, C, D
171Camelus dromedariusMutation(s): 0 
Gene Names: PGLYRP1 (PGLYRP, PGRP)
Find proteins for Q9GK12 (Camelus dromedarius)
Go to Gene View: PGLYRP1
Go to UniProtKB:  Q9GK12
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
C
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.044α = 90.00
b = 101.898β = 90.00
c = 162.675γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance