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PDBsum entry 2g6z

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2g6z
Jmol
Contents
Protein chain
147 a.a. *
Ligands
SO4 ×6
Waters ×39
* Residue conservation analysis
PDB id:
2g6z
Name: Hydrolase
Title: Crystal structure of human dusp5
Structure: Dual specificity protein phosphatase 5. Chain: a, b, c. Fragment: residues 174-384. Synonym: dusp5, dual specificity protein phosphatase hvh3, tyrosine-protein phosphatase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.70Å     R-factor:   0.244     R-free:   0.291
Authors: S.J.Kim,S.E.Ryu
Key ref:
D.G.Jeong et al. (2007). Crystal structure of the catalytic domain of human DUSP5, a dual specificity MAP kinase protein phosphatase. Proteins, 66, 253-258. PubMed id: 17078075 DOI: 10.1002/prot.21224
Date:
26-Feb-06     Release date:   16-Jan-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q16690  (DUS5_HUMAN) -  Dual specificity protein phosphatase 5
Seq:
Struc:
384 a.a.
147 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: 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 2: 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     dephosphorylation   2 terms 
  Biochemical function     phosphatase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.21224 Proteins 66:253-258 (2007)
PubMed id: 17078075  
 
 
Crystal structure of the catalytic domain of human DUSP5, a dual specificity MAP kinase protein phosphatase.
D.G.Jeong, Y.H.Cho, T.S.Yoon, J.H.Kim, S.E.Ryu, S.J.Kim.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) C trace of the DUSP5-C structure (black) superimposed with that of VHR (red; pdb code, 1VHR). The regions of DUSP5-C that cannot be aligned are shown in green. The secondary structural elements of DUSP5-C are labeled black whereas the secondary structural elements unique to VHR are labeled red. GA indicates the position of the general acid loop. (b) The active site of DUSP5-C. The active site of DUSP5-C (ivory) is superimposed with that of MKP3 (grey). C263S-R269, D232, and bound sulfate ion are shown for DUSP5-C, whereas C293-R299 and D262 are shown for MKP3. The hydrogen bonding interactions for DUSP5-C are indicated with dotted lines. The residues of DUSP5-C are shown in black whereas those for MKP are labeled red. Some side-chains were omitted from the drawing for clarity. (c) C trace of the DUSP5-C structure (black) is superimposed with that of the MKP-3 structure (red; pdb code, 1MKP). The regions of DUSP5-C that cannot be aligned are shown in green. The secondary structural elements for DUSP5-C are shown in black, whereas the secondary structural elements unique to MKP-3 are shown in red. (d) Ribbon diagram of a DUSP5-C dimer. Protomers A and B are shown in magenta and grey, respectively. Catalytically active residues, C263(A) and C263(B) and bound sulfate ions are represented with ball-and-stick models. (e) Stereodiagram of the 2Fo-Fc electron density map around the active site superposed on the refined model. The map is contoured at 1.2 level. The residues are represented as a ball-and-stick model.
 
  The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 66, 253-258) copyright 2007.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19415758 D.G.Jeong, S.K.Jung, T.S.Yoon, E.J.Woo, J.H.Kim, B.C.Park, S.E.Ryu, and S.J.Kim (2009).
Crystal structure of the catalytic domain of human MKP-2 reveals a 24-mer assembly.
  Proteins, 76, 763-767.
PDB code: 3ezz
19578332 G.Molina, A.Vogt, A.Bakan, W.Dai, P.Queiroz de Oliveira, W.Znosko, T.E.Smithgall, I.Bahar, J.S.Lazo, B.W.Day, and M.Tsang (2009).
Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages.
  Nat Chem Biol, 5, 680-687.  
19770498 G.T.Lountos, J.E.Tropea, S.Cherry, and D.S.Waugh (2009).
Overproduction, purification and structure determination of human dual-specificity phosphatase 14.
  Acta Crystallogr D Biol Crystallogr, 65, 1013-1020.
PDB code: 2wgp
19664213 K.L.Kuntz-Melcavage, R.M.Brucklacher, P.S.Grigson, W.M.Freeman, and K.E.Vrana (2009).
Gene expression changes following extinction testing in a heroin behavioral incubation model.
  BMC Neurosci, 10, 95.  
18855677 A.Bakan, J.S.Lazo, P.Wipf, K.M.Brummond, and I.Bahar (2008).
Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.
  Curr Med Chem, 15, 2536-2544.  
17496916 D.M.Owens, and S.M.Keyse (2007).
Differential regulation of MAP kinase signalling by dual-specificity protein phosphatases.
  Oncogene, 26, 3203-3213.  
17400920 X.Tao, and L.Tong (2007).
Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5.
  Protein Sci, 16, 880-886.
PDB codes: 2ouc 2oud
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.