5J4F

Crystal structure of the N-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori

Sim, D.W.Kim, J.H.Kim, H.Y.Jang, J.H.Lee, W.C.Kim, E.H.Park, P.J.Lee, K.H.Won, H.S.

(2016) FEBS Lett 590: 2997-3004

  • DOI: https://doi.org/10.1002/1873-3468.12332
  • Primary Citation of Related Structures:  
    5J4F, 5J4G

  • PubMed Abstract: 

    We solved the crystal structure of a functionally uncharacterized protein, HP0902, from Helicobacter pylori. Its structure demonstrated an all-β cupin fold that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. In contrast, isothermal titration calorimetry and NMR titration demonstrated that HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins. This report constitutes the first identification of an LPS-interacting protein, both in the cupin family and in H. pylori. Furthermore, identification of the ability of HP0902 to bind LPS uncovers a putative role for this protein in H. pylori pathogenicity.


  • Organizational Affiliation

    Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical and Health Science, Konkuk University, Chungbuk, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
119Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_0902
UniProt
Find proteins for O25562 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25562 
Go to UniProtKB:  O25562
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25562
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.512α = 90
b = 78.643β = 112.22
c = 41.404γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata processing
SCALAdata scaling
MOLREPphasing
SHELXDEmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description