3L3P

Crystal structure of the C-terminal domain of Shigella type III effector IpaH9.8, with a novel domain swap

• PDB DOI: https://doi.org/10.2210/pdb3L3P/pdb

• Classification: LIGASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-17 Released: 2010-09-08 
• Deposition Author(s): Seyedarabi, A., Sullivan, J.A., Sasakawa, C., Pickersgill, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.311 
• R-Value Work: 0.289 
• R-Value Observed: 0.290 

Literature

A disulfide driven domain swap switches off the activity of Shigella IpaH9.8 E3 ligase

Seyedarabi, A., Sullivan, J.A., Sasakawa, C., Pickersgill, R.W.

(2010) FEBS Lett 584: 4163-4168

• PubMed: 20831869 
• DOI: https://doi.org/10.1016/j.febslet.2010.09.006
• Primary Citation of Related Structures:  
  3L3P


• PubMed Abstract: 
  

  We show that the monomeric form of Shigella IpaH9.8 E3 ligase catalyses the ubiquitination of human U2AF35 in vitro, providing a molecular mechanism for the observed in vivo effect. We further discover that under non-reducing conditions IpaH9.8 undergoes a domain swap driven by the formation of a disulfide bridge involving the catalytic cysteine and that this dimer is unable to catalyse the ubiquitination of U2AF35. The crystal structure of the domain-swapped dimer is presented. The redox inactivation of IpaH9.8 could be a mechanism of regulating the activity of the IpaH9.8 E3 ligase in response to cell damage so that the host cell in which the bacteria resides is maintained in a benign state suitable for bacterial survival.

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Organizational Affiliation: 

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.46 kDa 
• Atom Count: 2,109 
• Modelled Residue Count: 263 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IpaH9.8	A	293	Shigella flexneri	Mutation(s): 0  Gene Names: ipaH9.8 EC: 6.3.2.19
UniProt
Find proteins for Q8VSC3 (Shigella flexneri) Explore Q8VSC3  Go to UniProtKB:  Q8VSC3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.311 
• R-Value Work: 0.289 
• R-Value Observed: 0.290 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.659	α = 90
b = 92.659	β = 90
c = 135.612	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Seyedarabi, A., Sullivan, J.A., Sasakawa, C., Pickersgill, R.W.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description