spacer
spacer

PDBsum entry 2i3u

Go to PDB code: 
protein links
Hydrolase PDB id
2i3u
Jmol
Contents
Protein chain
276 a.a. *
Waters ×204
* Residue conservation analysis
PDB id:
2i3u
Name: Hydrolase
Title: Structural studies of protein tyrosine phosphatase beta cata domain in complex with inhibitors
Structure: Receptor-type tyrosine-protein phosphatase beta. Chain: a. Fragment: catalytic domain, residues 1662-1973. Synonym: protein-tyrosine phosphatase beta, r-ptp-beta. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ptprb, ptpb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.187     R-free:   0.226
Authors: A.G.Evdokimov,M.E.Pokross,R.L.Walter,M.Mekel
Key ref:
A.G.Evdokimov et al. (2006). Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery. Acta Crystallogr D Biol Crystallogr, 62, 1435-1445. PubMed id: 17139078 DOI: 10.1107/S0907444906037784
Date:
20-Aug-06     Release date:   29-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23467  (PTPRB_HUMAN) -  Receptor-type tyrosine-protein phosphatase beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1997 a.a.
276 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
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     2 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444906037784 Acta Crystallogr D Biol Crystallogr 62:1435-1445 (2006)
PubMed id: 17139078  
 
 
Engineering the catalytic domain of human protein tyrosine phosphatase beta for structure-based drug discovery.
A.G.Evdokimov, M.Pokross, R.Walter, M.Mekel, B.Cox, C.Li, R.Bechard, F.Genbauffe, R.Andrews, C.Diven, B.Howard, V.Rastogi, J.Gray, M.Maier, K.G.Peters.
 
  ABSTRACT  
 
Protein tyrosine phosphatases (PTPs) play roles in many biological processes and are considered to be important targets for drug discovery. As inhibitor development has proven challenging, crystal structure-based design will be very helpful to advance inhibitor potency and selectivity. Successful application of protein crystallography to drug discovery heavily relies on high-quality crystal structures of the protein of interest complexed with pharmaceutically interesting ligands. It is very important to be able to produce protein-ligand crystals rapidly and reproducibly for as many ligands as necessary. This study details our efforts to engineer the catalytic domain of human protein tyrosine phosphatase beta (HPTPbeta-CD) with properties suitable for rapid-turnaround crystallography. Structures of apo HPTPbeta-CD and its complexes with several novel small-molecule inhibitors are presented here for the first time.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Detailed view of the PTP -CD active site. (a) Hydrogen-bonding network (blue dashes) bridging the ligand (vanadate ion, balls-and-stick representation) and the protein (sticks). (b) Side view depicting additional interactions (magenta dashes) between the ligand and polar residues in the active site. The partial covalent bond between Cys1904 and the V atom is shown as an orange dashed line. (c) Side view of a pTyr mimetic (p-ethyl phenylsulfamic acid) bound in the active site of the enzyme. Relevant hydrogen bonds are shown as colored dashes.
Figure 4.
Figure 4 Transition of the WPD-loop between open (light brown) and closed (green) states. The ligand (sulfamic acid, yellow) is shown in ball-and-stick representation and relevant protein residues are shown as sticks colored according to the loop state. The catalytically important water molecule is shown as a red sphere.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1435-1445) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20236928 T.A.Brandão, A.C.Hengge, and S.J.Johnson (2010).
Insights into the reaction of protein-tyrosine phosphatase 1B: crystal structures for transition state analogs of both catalytic steps.
  J Biol Chem, 285, 15874-15883.
PDB codes: 3i7z 3i80
18298793 L.Tabernero, A.R.Aricescu, E.Y.Jones, and S.E.Szedlacsek (2008).
Protein tyrosine phosphatases: structure-function relationships.
  FEBS J, 275, 867-882.  
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 codes are shown on the right.