3GUQ

Crystal structure of novel carcinogenic factor of H. pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the Helicobacter pylori-carcinogenic TNF-alpha-inducing protein.

Tsuge, H.Tsurumura, T.Utsunomiya, H.Kise, D.Kuzuhara, T.Watanabe, T.Fujiki, H.Suganuma, M.

(2009) Biochem Biophys Res Commun 388: 193-198

  • DOI: https://doi.org/10.1016/j.bbrc.2009.07.121
  • Primary Citation of Related Structures:  
    3GUQ

  • PubMed Abstract: 

    Stomach cancer is strongly associated with infection by Helicobacter pylori. In 2005, we identified a new H. pylori gene encoding a TNF-alpha inducing protein (Tipalpha) that acts as a carcinogenic factor. Tipalpha is secreted from H. pylori as a homodimer whose subunits are linked by disulfide bonds. We also characterized a Tipalpha deletion mutant (del-Tipalpha) that lacks the N-terminal six amino acid residues (LQACTC), including two cysteines (C5 and C7) that form disulfide bonds, but nonetheless shows a weak ability to induce TNF-alpha expression. Here we report that del-Tipalpha has a novel elongated structure containing a 40-A-long alpha helix, and forms a heart-shaped homodimer via non-covalent bonds. Moreover, their circular dichroism spectra strongly suggest that the structures of the del-Tipalpha and Tipalpha homodimers are very similar. del-Tipalpha's unique mode of dimer formation provides important insight into protein-protein interactions and into the mechanism underlying the carcinogenicity of H. pylori infection.


  • Organizational Affiliation

    Institute for Health Sciences, Tokushima Bunri University, Yamashiro-Cho, Tokushima 770-8514, Japan. tsuge@tokushima.bunri-u.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein166Helicobacter pyloriMutation(s): 0 
Gene Names: HP0596HP_0596
UniProt
Find proteins for O25318 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25318 
Go to UniProtKB:  O25318
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25318
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.518α = 90
b = 69.518β = 90
c = 69.161γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references