2CB3

Crystal structure of peptidoglycan recognition protein-LE in complex with tracheal cytotoxin (monomeric diaminopimelic acid-type peptidoglycan)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Preferential Recognition of Diaminopimelic Acid-Type Peptidoglycan by a Subset of Peptidoglycan Recognition Proteins

Lim, J.-H.Kim, M.-S.Kim, H.-E.Yano, T.Oshima, Y.Aggarwal, K.Goldman, W.E.Silverman, N.Kurata, S.Oh, B.-H.

(2006) J Biol Chem 281: 8286

  • DOI: https://doi.org/10.1074/jbc.M513030200
  • Primary Citation of Related Structures:  
    2CB3

  • PubMed Abstract: 

    Drosophila peptidoglycan recognition protein (PGRP)-LCx and -LCa are receptors that preferentially recognize meso-diaminopimelic acid (DAP)-type peptidoglycan (PGN) present in Gram-negative bacteria over lysine-type PGN of gram-positive bacteria and initiate the IMD signaling pathway, whereas PGRP-LE plays a synergistic role in this process of innate immune defense. How these receptors can distinguish the two types of PGN remains unclear. Here the structure of the PGRP domain of Drosophila PGRP-LE in complex with tracheal cytotoxin (TCT), the monomeric DAP-type PGN, reveals a buried ionic interaction between the unique carboxyl group of DAP and a previously unrecognized arginine residue. This arginine is conserved in the known DAP-type PGN-interacting PGRPs and contributes significantly to the affinity of the protein for the ligand. Unexpectedly, TCT induces infinite head-to-tail dimerization of PGRP-LE, in which the disaccharide moiety, but not the peptide stem, of TCT is positioned at the dimer interface. A sequence comparison suggests that TCT induces heterodimerization of the ectodomains of PGRP-LCx and -LCa in a closely analogous manner to prime the IMD signaling pathway, except that the heterodimer formation is nonperpetuating.


  • Organizational Affiliation

    Center for Biomolecular Recognition and Division of Molecular and Life Science, Department of Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDOGLYCAN-RECOGNITION PROTEIN-LE
A, B, C, D
175Drosophila melanogasterMutation(s): 1 
UniProt
Find proteins for Q9VXN9 (Drosophila melanogaster)
Explore Q9VXN9 
Go to UniProtKB:  Q9VXN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VXN9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.53α = 90
b = 217.53β = 90
c = 217.53γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-26
    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, Other, Refinement description