2EAX

Crystal structure of human PGRP-IBETAC in complex with glycosamyl muramyl pentapeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins

Cho, S.Wang, Q.Swaminathan, C.P.Hesek, D.Lee, M.Boons, G.J.Mobashery, S.Mariuzza, R.A.

(2007) Proc.Natl.Acad.Sci.Usa 104: 8761-8766

  • DOI: 10.1073/pnas.0701453104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptidoglycan recognition proteins (PGRPs) are highly conserved pattern-recognition molecules of the innate immune system that bind bacterial peptidoglycans (PGNs), which are polymers of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid ...

    Peptidoglycan recognition proteins (PGRPs) are highly conserved pattern-recognition molecules of the innate immune system that bind bacterial peptidoglycans (PGNs), which are polymers of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by short peptide stems. Human PRGPs are bactericidal against pathogenic and nonpathogenic Gram-positive bacteria, but not normal flora bacteria. Like certain glycopeptide antibiotics (e.g., vancomycin), PGRPs kill bacteria by directly interacting with their cell wall PGN, thereby interfering with PGN maturation. To better understand the bactericidal mechanism of PGRPs, we determined the crystal structure of the C-terminal PGN-binding domain of human PGRP-I beta in complex with NAG-NAM-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala, a synthetic glycopeptide comprising a complete PGN repeat. This structure, in conjunction with the previously reported NMR structure of a dimeric PGN fragment, permitted identification of major conformational differences between free and PGRP-bound PGN with respect to the relative orientation of saccharide and peptide moieties. These differences provided structural insights into the bactericidal mechanism of human PGRPs. On the basis of molecular modeling, we propose that these proteins disrupt cell wall maturation not only by sterically encumbering access of biosynthetic enzymes to the nascent PGN chains, but also by locking PGN into a conformation that prevents formation of cross-links between peptide stems in the growing cell wall.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, W. M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan recognition protein-I-beta
A, B, C
164Homo sapiensMutation(s): 0 
Gene Names: PGLYRP4 (PGRPIB)
Find proteins for Q96LB8 (Homo sapiens)
Go to Gene View: PGLYRP4
Go to UniProtKB:  Q96LB8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLYCOSAMYL MURAMYL PENTAPEPTIDE
L
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMV
Query on AMV

Download SDF File 
Download CCD File 
L
METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
C12 H21 N O8
UXEQYDNCHCKBIL-PKKPQKKZSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FGA
Query on FGA
L
D-gamma-peptide, C-delta linkingC5 H9 N O4

--

DAL
Query on DAL
L
D-PEPTIDE LINKINGC3 H7 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.940α = 90.00
b = 61.390β = 96.45
c = 97.950γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CrystalCleardata scaling
CNSrefinement
CrystalCleardata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-02-03 
  • Released Date: 2007-10-02 
  • Deposition Author(s): Cho, S.

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references, Derived calculations, Non-polymer description
  • Version 1.3: 2011-09-14
    Type: Non-polymer description
  • Version 1.4: 2011-09-21
    Type: Source and taxonomy, Structure summary
  • Version 1.5: 2014-12-17
    Type: Atomic model, Derived calculations