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PDBsum entry 3f99

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protein ligands links
Hydrolase PDB id
3f99
Jmol
Contents
Protein chain
282 a.a. *
Ligands
TRS
Waters ×268
* Residue conservation analysis
PDB id:
3f99
Name: Hydrolase
Title: W354f yersinia enterocolitica ptpase apo form
Structure: Tyrosine-protein phosphatase yoph. Chain: a. Fragment: yoph catalytic domain: unp residues 164-468. Synonym: virulence protein. Engineered: yes. Mutation: yes
Source: Yersinia enterocolitica (type o:9). Organism_taxid: 34055. Strain: w22703 / serotype o:9 / biotype 2. Gene: yoph, yop51. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.65Å     R-factor:   0.198     R-free:   0.234
Authors: T.A.S.Brandao,H.Robinson,S.J.Johnson,A.C.Hengge
Key ref: T.A.Brandão et al. (2009). Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures. J Am Chem Soc, 131, 778-786. PubMed id: 19140798
Date:
13-Nov-08     Release date:   20-Jan-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15273  (YOPH_YEREN) -  Tyrosine-protein phosphatase YopH
Seq:
Struc:
468 a.a.
282 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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    
 
 
J Am Chem Soc 131:778-786 (2009)
PubMed id: 19140798  
 
 
Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures.
T.A.Brandão, H.Robinson, S.J.Johnson, A.C.Hengge.
 
  ABSTRACT  
 
Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 A structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO](2) core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.
 

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
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.