2H7O | pdb_00002h7o

Crystal structure of the Rho-GTPase binding domain of YpkA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.237 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2H7O

This is version 1.3 of the entry. See complete history

Literature

Yersinia virulence depends on mimicry of host rho-family nucleotide dissociation inhibitors.

Prehna, G.Ivanov, M.I.Bliska, J.B.Stebbins, C.E.

(2006) Cell 126: 869-880

  • DOI: https://doi.org/10.1016/j.cell.2006.06.056
  • Primary Citation Related Structures: 
    2H7O, 2H7V

  • PubMed Abstract: 

    Yersinia spp. cause gastroenteritis and the plague, representing historically devastating pathogens that are currently an important biodefense and antibiotic resistance concern. A critical virulence determinant is the Yersinia protein kinase A, or YpkA, a multidomain protein that disrupts the eukaryotic actin cytoskeleton. Here we solve the crystal structure of a YpkA-Rac1 complex and find that YpkA possesses a Rac1 binding domain that mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases. YpkA inhibits nucleotide exchange in Rac1 and RhoA, and mutations that disrupt the YpkA-GTPase interface abolish this activity in vitro and impair in vivo YpkA-induced cytoskeletal disruption. In cell culture experiments, the kinase and the GDI domains of YpkA act synergistically to promote cytoskeletal disruption, and a Y. pseudotuberculosis mutant lacking YpkA GDI activity shows attenuated virulence in a mouse infection assay. We conclude that virulence in Yersinia depends strongly upon mimicry of host GDI proteins by YpkA.


  • Organizational Affiliation
    • Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA.

Macromolecule Content 

  • Total Structure Weight: 34.45 kDa 
  • Atom Count: 2,445 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 303 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein kinase ypkA303Yersinia pseudotuberculosisMutation(s): 0 
Gene Names: ypkA
EC: 2.7.11.1
UniProt
Find proteins for Q05608 (Yersinia pseudotuberculosis serotype I (strain IP32953))
Explore Q05608 
Go to UniProtKB:  Q05608
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05608
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.237 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.272 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.009α = 90
b = 60.009β = 90
c = 402.022γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references