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PDBsum entry 3s3f

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
3s3f
Jmol
Contents
Protein chains
287 a.a.
Ligands
1BO ×2
IPA ×2
VO4
BU1
Waters ×90
PDB id:
3s3f
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of the catalytic domain of ptp10d from dro melanogaster with a small molecule inhibitor vanadate
Structure: Tyrosine-protein phosphatase 10d. Chain: a, b. Fragment: unp residues 1250-1533. Synonym: receptor-linked protein-tyrosine phosphatase 10d, engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: cg1817, ptp10d. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.70Å     R-factor:   0.240     R-free:   0.272
Authors: L.L.Madan,B.Gopal
Key ref: L.L.Madan and B.Gopal (2011). Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D. Biochemistry, 50, 10114-10125. PubMed id: 22007620
Date:
18-May-11     Release date:   02-Nov-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P35992  (PTP10_DROME) -  Tyrosine-protein phosphatase 10D
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1631 a.a.
287 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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    
 
 
Biochemistry 50:10114-10125 (2011)
PubMed id: 22007620  
 
 
Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D.
L.L.Madan, B.Gopal.
 
  ABSTRACT  
 
The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.