1KZ7

Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental Isoform of Human Cdc42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange.

Rossman, K.L.Worthylake, D.K.Snyder, J.T.Siderovski, D.P.Campbell, S.L.Sondek, J.

(2002) EMBO J 21: 1315-1326

  • DOI: 10.1093/emboj/21.6.1315
  • Primary Citation of Related Structures:  
    1KZ7, 1KZG

  • PubMed Abstract: 
  • Dbl-related oncoproteins are guanine nucleotide exchange factors (GEFs) specific for Rho guanosine triphosphatases (GTPases) and invariably possess tandem Dbl (DH) and pleckstrin homology (PH) domains. While it is known that the DH domain is the principal catalytic subunit, recent biochemical data indicate that for some Dbl-family proteins, such as Dbs and Trio, PH domains may cooperate with their associated DH domains in promoting guanine nucleotide exchange of Rho GTPases ...

    Dbl-related oncoproteins are guanine nucleotide exchange factors (GEFs) specific for Rho guanosine triphosphatases (GTPases) and invariably possess tandem Dbl (DH) and pleckstrin homology (PH) domains. While it is known that the DH domain is the principal catalytic subunit, recent biochemical data indicate that for some Dbl-family proteins, such as Dbs and Trio, PH domains may cooperate with their associated DH domains in promoting guanine nucleotide exchange of Rho GTPases. In order to gain an understanding of the involvement of these PH domains in guanine nucleotide exchange, we have determined the crystal structure of a DH/PH fragment from Dbs in complex with Cdc42. The complex features the PH domain in a unique conformation distinct from the PH domains in the related structures of Sos1 and Tiam1.Rac1. Consequently, the Dbs PH domain participates with the DH domain in binding Cdc42, primarily through a set of interactions involving switch 2 of the GTPase. Comparative sequence analysis suggests that a subset of Dbl-family proteins will utilize their PH domains similarly to Dbs.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS AC353Mus musculusMutation(s): 10 
Gene Names: DbsMcf2l
Find proteins for Q64096 (Mus musculus)
Explore Q64096 
Go to UniProtKB:  Q64096
NIH Common Fund Data Resources
IMPC:  MGI:103263
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CDC42 HOMOLOG BD188Homo sapiensMutation(s): 1 
Gene Names: CDC42
EC: 3.6.5.2
Find proteins for P60953 (Homo sapiens)
Explore P60953 
Go to UniProtKB:  P60953
NIH Common Fund Data Resources
PHAROS:  P60953
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.5α = 90
b = 87.98β = 90
c = 230.51γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance