2H7V

Co-crystal structure of YpkA-Rac1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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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: 10.1016/j.cell.2006.06.056
  • Primary Citation of 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 ...

    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: 
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Migration-inducing protein 5A, B188Homo sapiensMutation(s): 1 
Gene Names: MIG5, RAC1, TC25
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens)
Explore P63000 
Go to UniProtKB:  P63000
PHAROS:  P63000
Entity Groups  
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UniProt GroupP63000
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein kinase ypkAC, D303Yersinia 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • R-Value Observed: 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations