2H7V

Co-crystal structure of YpkA-Rac1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.cell.2006.06.056
  • Primary Citation of Related Structures:  

  • 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 Yp ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Migration-inducing protein 5
A, B
188Homo sapiensMutation(s): 1 
Gene Names: RAC1 (TC25)
Find proteins for P63000 (Homo sapiens)
Go to Gene View: RAC1
Go to UniProtKB:  P63000
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein kinase ypkA
C, D
303Yersinia pseudotuberculosis serotype I (strain IP32953)Mutation(s): 0 
Gene Names: ypkA
EC: 2.7.11.1
Find proteins for Q05608 (Yersinia pseudotuberculosis serotype I (strain IP32953))
Go to UniProtKB:  Q05608
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.398α = 92.08
b = 75.519β = 103.38
c = 99.772γ = 115.79
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance