4X5U

X-ray crystal structure of CagL at pH 4.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Integrin Engagement by the Helical RGD Motif of the Helicobacter pylori CagL Protein Is Regulated by pH-induced Displacement of a Neighboring Helix.

Bonsor, D.A.Pham, K.T.Beadenkopf, R.Diederichs, K.Haas, R.Beckett, D.Fischer, W.Sundberg, E.J.

(2015) J Biol Chem 290: 12929-12940

  • DOI: https://doi.org/10.1074/jbc.M115.641829
  • Primary Citation of Related Structures:  
    4X5U

  • PubMed Abstract: 

    Arginine-aspartate-glycine (RGD) motifs are recognized by integrins to bridge cells to one another and the extracellular matrix. RGD motifs typically reside in exposed loop conformations. X-ray crystal structures of the Helicobacter pylori protein CagL revealed that RGD motifs can also exist in helical regions of proteins. Interactions between CagL and host gastric epithelial cell via integrins are required for the translocation of the bacterial oncoprotein CagA. Here, we have investigated the molecular basis of the CagL-host cell interactions using structural, biophysical, and functional analyses. We solved an x-ray crystal structure of CagL that revealed conformational changes induced by low pH not present in previous structures. Using analytical ultracentrifugation, we found that pH-induced conformational changes in CagL occur in solution and not just in the crystalline environment. By designing numerous CagL mutants based on all available crystal structures, we probed the functional roles of CagL conformational changes on cell surface integrin engagement. Together, our data indicate that the helical RGD motif in CagL is buried by a neighboring helix at low pH to inhibit CagL binding to integrin, whereas at neutral pH the neighboring helix is displaced to allow integrin access to the CagL RGD motif. This novel molecular mechanism of regulating integrin-RGD motif interactions by changes in the chemical environment provides new insight to H. pylori-mediated oncogenesis.


  • Organizational Affiliation

    From the Institute of Human Virology and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cag pathogenicity island protein (Cag18)226Helicobacter pylori 26695Mutation(s): 0 
Gene Names: C694_02780HP_0539
UniProt
Find proteins for O25272 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25272 
Go to UniProtKB:  O25272
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25272
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.257 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.018α = 90
b = 63.018β = 90
c = 243.763γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
XDSdata scaling
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description