1UEF

Crystal Structure of Dok1 PTB Domain Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain

Shi, N.Ye, S.Bartlam, M.Yang, M.Wu, J.Liu, Y.Sun, F.Han, X.Peng, X.Qiang, B.Yuan, J.Rao, Z.

(2004) J.Biol.Chem. 279: 4962-4969

  • DOI: 10.1074/jbc.M311030200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dok1 is a common substrate of activated protein-tyrosine kinases. It is rapidly tyrosine-phosphorylated in response to receptor tyrosine activation and interacts with ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathw ...

    Dok1 is a common substrate of activated protein-tyrosine kinases. It is rapidly tyrosine-phosphorylated in response to receptor tyrosine activation and interacts with ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. In chronic myelogenous leukemia cells, it has shown constitutive phosphorylation. The N-terminal phosphotyrosine binding (PTB) domain of Dok1 can recognize and bind specifically to phosphotyrosine-containing motifs of receptors. Here we report the crystal structure of the Dok1 PTB domain alone and in complex with a phosphopeptide derived from RET receptor tyrosine kinase. The structure consists of a beta-sandwich composed of two nearly orthogonal, 7-stranded, antiparallel beta-sheets, and it is capped at one side by a C-terminal alpha-helix. The RET phosphopeptide binds to Dok1 via a surface groove formed between strand beta5 and the C-terminal alpha-helix of the PTB domain. The structures reveal the molecular basis for the specific recognition of RET by the Dok1 PTB domain. We also show that Dok1 does not recognize peptide sequences from TrkA and IL-4, which are recognized by Shc and IRS1, respectively.


    Organizational Affiliation

    Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Docking protein 1
A, B
127Mus musculusMutation(s): 0 
Gene Names: Dok1 (Dok)
Find proteins for P97465 (Mus musculus)
Go to UniProtKB:  P97465
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret
C, D
13Mus musculusMutation(s): 0 
Gene Names: Ret
EC: 2.7.10.1
Find proteins for P35546 (Mus musculus)
Go to UniProtKB:  P35546
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.482α = 90.00
b = 55.720β = 90.00
c = 99.126γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
HKL-2000data collection
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance