3CVR

Crystal structure of the full length IpaH3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of a Shigella effector reveals a new class of ubiquitin ligases

Zhu, Y., Li, H., Hu, L., Wang, J., Zhou, Y., Pang, Z., Liu, L., Shao, F.

(2008) Nat.Struct.Mol.Biol. 15: 1302-1308

  • DOI: 10.1038/nsmb.1517

  • PubMed Abstract: 

    • Bacterial pathogens have evolved effector proteins with ubiquitin E3 ligase activities through structural mimicking. Here we report the crystal structure of the Shigella flexneri type III effector IpaH3, a member of the leucine-rich repeat (LRR)-cont ...

    Bacterial pathogens have evolved effector proteins with ubiquitin E3 ligase activities through structural mimicking. Here we report the crystal structure of the Shigella flexneri type III effector IpaH3, a member of the leucine-rich repeat (LRR)-containing bacterial E3 family. The LRR domain is structurally similar to Yersinia pestis YopM and potentially binds to substrates. The structure of the C-terminal E3 domain differs from the typical RING- and HECT-type E3s. IpaH3 synthesizes a Lys48-linked ubiquitin chain, and the reaction requires noncovalent binding between ubiquitin and a specific E2, UbcH5. Free ubiquitin serves as an acceptor for IpaH3-catalyzed ubiquitin transfer. Cys363 within a conserved CXD motif acts as a nucleophile to catalyze ubiquitin transfer through a transthiolation reaction. The D365N mutant is devoid of E3 activities but turns into a potent ubiquitin-E2 thioesterase. Our analysis establishes a structurally and mechanistically distinct class of ubiquitin ligases found exclusively in pathogenic or symbiotic bacteria.

    Organizational Affiliation: 

    National Institute of Biological Sciences, 7# Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Invasion plasmid antigen
A
571Shigella flexneriMutation(s): 0 
Gene Names: ipaH3
EC: 2.3.2.27
Find proteins for Q83RJ4 (Shigella flexneri)
Go to UniProtKB:  Q83RJ4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.251 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 154.190α = 90.00
b = 154.190β = 90.00
c = 85.870γ = 90.00
Software Package:
Software NamePurpose
SCALAdata processing
ADSCdata collection
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-04-19 
  • Released Date: 2008-11-11 
  • Deposition Author(s): Zhu, Y., Shao, F.

Revision History 

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance