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PDBsum entry 2gwo

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protein Protein-protein interface(s) links
Hydrolase PDB id
2gwo
Jmol
Contents
Protein chain
169 a.a. *
Waters ×260
* Residue conservation analysis
PDB id:
2gwo
Name: Hydrolase
Title: Crystal structure of tmdp
Structure: Dual specificity protein phosphatase 13. Chain: a, b, c, d. Synonym: testis- and skeletal-muscle-specific dsp, dual specificity phosphatase skrp4, tmdp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dusp13, tmdp. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.198     R-free:   0.250
Authors: S.J.Kim,S.E.Ryu,J.H.Kim
Key ref:
S.J.Kim et al. (2007). Crystal structure of human TMDP, a testis-specific dual specificity protein phosphatase: implications for substrate specificity. Proteins, 66, 239-245. PubMed id: 17044055 DOI: 10.1002/prot.21197
Date:
05-May-06     Release date:   20-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UII6  (DUS13_HUMAN) -  Dual specificity protein phosphatase 13 isoform B
Seq:
Struc:
198 a.a.
169 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.1.3.16  - Protein-serine/threonine phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [a protein]-serine/threonine phosphate + H2O = [a protein]- serine/threonine + phosphate
[a protein]-serine/threonine phosphate
+ H(2)O
= [a protein]- serine/threonine
+ phosphate
   Enzyme class 3: E.C.3.1.3.48  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+ phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptidyl-tyrosine dephosphorylation   5 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.21197 Proteins 66:239-245 (2007)
PubMed id: 17044055  
 
 
Crystal structure of human TMDP, a testis-specific dual specificity protein phosphatase: implications for substrate specificity.
S.J.Kim, D.G.Jeong, T.S.Yoon, J.H.Son, S.K.Cho, S.E.Ryu, J.H.Kim.
 
  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 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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall structure of TMDP. (a) The TMDP structure is presented as a ribbon diagram. Secondary structural elements are labeled on the drawing. The active site cysteine is drawn as a ball-and-stick representation. Boundaries of the secondary structural elements are 1 (28-37), 1 (42-50), 2 (53-56), 2 (58-62), 3 (64-69), 3 (74-77), 4 (86-89), 4 (98-101), 5 (103-128), 5 (104-107), 6 (144-157), 7 (161-169), 8 (178-193). (b) The 2Fo-Fc electron density map around the active site is superimposed with the refined model. The map is contoured at the 1.1 level. (c) Structural comparison of TMDP (thick line) with VHR (thin line). C traces of two structures are superimposed using the O program.[18] The point of view is the same as in panel (a). The regions of TMDP that cannot be aligned are green whereas the corresponding regions of VHR are red. The position of C atom of Cys138 in TMDP is represented as a ball and labeled in the stereodiagram.
Figure 3.
Figure 3. A structural comparison of TMDP, VHR, and PTP1B. (a) TMDP is superposed with VHR complexed with its phospho-peptide (PDB code 1J4X). The worm model of TMDP is cyan whereas those of VHR and phospho-peptide are magenta and orange, respectively. The residues that contribute to the entrance to active sites are drawn by ball-and-stick model and labeled (TMDP: green, VHR: red, phosphorylated residues: grey). (b) The electrostatic potential surfaces of TMDP, VHR (PDB code: 1J4X) complexed with its phospho-peptide and PTP1B (PDB code: 2HNP) are compared. In a VHR complex, phospho-peptide is represented by stick model. Positive and negative potentials are blue and red, respectively. The dotted line indicates the borders that are rimmed by the surrounding loops to the active site. The surrounding loops and the active site cysteine residues are labeled in green and in black, respectively. The electrostatic surface potentials were calculated with contours from -10 (red) to + 10 (blue) kTe^-1 (k, Boltzmann's constant; T, temperature; e, electron) and with an exterior dielectric constant of 80. (c) The sliced views of active sites of TMDP, VHR (PDB code: 1VHR) and PTP1B (PDB code: 1AAX). The molecular surface diagrams are drawn as a basket-weaved model by using the VOIDOO program.[28] The molecular surfaces near the active sites reveal that the pocket depth of TMDP is shallow when compared with those of PTP1B and VHR. The surfaces of TMDP, VHR, and PTP1B are violet, navy, and orange, respectively.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 66, 239-245) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21543850 G.T.Lountos, J.E.Tropea, and D.S.Waugh (2011).
Structure of human dual-specificity phosphatase 27 at 2.38 Å resolution.
  Acta Crystallogr D Biol Crystallogr, 67, 471-479.
PDB code: 2y96
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.