1TWQ

Crystal structure of the C-terminal PGN-binding domain of human PGRP-Ialpha in complex with PGN analog muramyl tripeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for peptidoglycan binding by peptidoglycan recognition proteins

Guan, R.Roychowdhury, A.Ember, B.Kumar, S.Boons, G.-A.Mariuzza, R.A.

(2004) Proc.Natl.Acad.Sci.USA 101: 17168-17173

  • DOI: 10.1073/pnas.0407856101

  • PubMed Abstract: 
  • Peptidoglycan (PGN) recognition proteins (PGRPs) are pattern-recognition receptors of the innate immune system that bind and, in some cases, hydrolyze bacterial PGNs. We determined the crystal structure, at 2.30-A resolution, of the C-terminal PGN-bi ...

    Peptidoglycan (PGN) recognition proteins (PGRPs) are pattern-recognition receptors of the innate immune system that bind and, in some cases, hydrolyze bacterial PGNs. We determined the crystal structure, at 2.30-A resolution, of the C-terminal PGN-binding domain of human PGRP-Ialpha in complex with a muramyl tripeptide representing the core of lysine-type PGNs from Gram-positive bacteria. The peptide stem of the ligand is buried at the deep end of a long binding groove, with N-acetylmuramic acid situated in the middle of the groove, whose shallow end can accommodate a linked N-acetylglucosamine. Although most interactions are with the peptide, the glycan moiety also seems to be essential for specific recognition by PGRPs. Conservation of key PGN-contacting residues shows that all PGRPs employ this basic PGN-binding mode. The structure pinpoints variable residues that likely mediate discrimination between lysine- and diaminopimelic acid-type PGNs. We also propose a mechanism for PGN hydrolysis by Zn(2+)-containing PGRPs.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, W. M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
peptidoglycan recognition protein-I-alpha
A
165Homo sapiensGene Names: PGLYRP3 (PGRPIA)
Find proteins for Q96LB9 (Homo sapiens)
Go to Gene View: PGLYRP3
Go to UniProtKB:  Q96LB9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
muramyl tripeptide
P
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P
NON-POLYMERH2 N

--

AMU
Query on AMU
P
D-SACCHARIDEC11 H19 N O8

--

GMA
Query on GMA
P
L-PEPTIDE LINKINGC5 H10 N2 O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.511α = 90.00
b = 104.511β = 90.00
c = 42.050γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata reduction
CNSrefinement
AMoREphasing
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-11
    Type: Advisory, Refinement description