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: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.5 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 U S A 101: 17168-17173

  • DOI: 10.1073/pnas.0407856101
  • Primary Citation of Related Structures:  
    1TWQ

  • 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-binding domain of human PGRP-Ialpha in complex with a muramyl tripeptide representing the core of lysine-type PGNs from Gram-positive bacteria ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
peptidoglycan recognition protein-I-alpha A165Homo sapiensMutation(s): 0 
Gene Names: PGLYRP3, PGRPIA
Find proteins for Q96LB9 (Homo sapiens)
Explore Q96LB9 
Go to UniProtKB:  Q96LB9
NIH Common Fund Data Resources
PHAROS:  Q96LB9
GTEx:  ENSG00000159527
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
muramyl tripeptide P5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI
Download Ideal Coordinates CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GMA
Query on GMA		PL-PEPTIDE LINKINGC5 H10 N2 O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.511α = 90
b = 104.511β = 90
c = 42.05γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
AMoREphasing
CNSrefinement
CrystalCleardata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary