2GWO

crystal structure of TMDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human TMDP, a testis-specific dual specificity protein phosphatase: implications for substrate specificity

Kim, S.J.Jeong, D.G.Yoon, T.S.Son, J.H.Cho, S.K.Ryu, S.E.Kim, J.H.

(2007) Proteins 66: 239-245

  • DOI: 10.1002/prot.21197

  • PubMed Abstract: 
  • The testis- and skeletal-muscle-specific dual-specificity phosphatase (TMDP) is a member of the dual-specificity phosphatase (DSP) subgroup of protein tyrosine phosphatases. TMDP has similar activities toward both tyrosine and threonine phosphorylate ...

    The testis- and skeletal-muscle-specific dual-specificity phosphatase (TMDP) is a member of the dual-specificity phosphatase (DSP) subgroup of protein tyrosine phosphatases. TMDP has similar activities toward both tyrosine and threonine phosphorylated substrates, and is supposed to be involved in spermatogenesis. Here, we report the crystal structure of human TMDP at a resolution of 2.4 A. In spite of high sequence similarity with other DSPs, the crystal structure of TMDP shows distinct structural motifs and surface properties. In TMDP, the alpha1-beta1 loop, a substrate recognition motif is located further away from the active site loop in comparison to prototype DSP Vaccinia H1 related phophatase (VHR), which preferentially dephosphorylates tyrosine phosphorylated substrates and down-regulates MAP kinase signaling. Residues in the active site residues of TMDP are smaller in size and more hydrophobic than those of VHR. In addition, TMDP cannot be aligned with VHR in loop beta3-alpha4. These differences in the active site of TMDP result in a flat and wide pocket structure, allowing equal binding of phosphotyrosine and phosphothreonine substrates.


    Organizational Affiliation

    Center for Cellular Switch Protein Structure, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity protein phosphatase 13
A, B, C, D
198Homo sapiensGene Names: DUSP13 (DUSP13B, TMDP)
EC: 3.1.3.48, 3.1.3.16
Find proteins for Q9UII6 (Homo sapiens)
Go to Gene View: DUSP13
Go to UniProtKB:  Q9UII6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.586α = 90.00
b = 72.240β = 99.66
c = 89.896γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance