PDBsum entry 4zi4

Hydrolase

PDB id: 4zi4

Contents

Protein chain

282 a.a.

Ligands

DVG

VO4

Waters ×392

PDB id:

4zi4

Name:

Hydrolase

Title:

Yoph w354h yersinia enterocolitica ptpase bond with divanadate glycerol ester in the active site

Structure:

Tyrosine-protein phosphatase yoph. Chain: a. Fragment: catalytic domain (unp residues 164-468). Synonym: virulence protein. Engineered: yes. Mutation: yes

Source:

Yersinia enterocolitica. Organism_taxid: 630. Strain: dh5a. Gene: yoph, yop51. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.12Å R-factor: 0.142 R-free: 0.159

Authors:

G.E.Moise,S.J.Johnson,A.C.Hengge

Key ref:

G.Moise et al. (2015). Conservative tryptophan mutants of the protein tyrosine phosphatase YopH exhibit impaired WPD-loop function and crystallize with divanadate esters in their active sites. Biochemistry, 54, 6490-6500. PubMed id: 26445170 DOI: 10.1021/acs.biochem.5b00496

Date:

27-Apr-15 Release date: 28-Oct-15

Protein chain

P15273  (YOPH_YEREN) -  Tyrosine-protein phosphatase YopH from Yersinia enterocolitica

Seq: 468 a.a.

Struc: 282 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1021/acs.biochem.5b00496

Biochemistry 54:6490-6500 (2015)

PubMed id: 26445170

Conservative tryptophan mutants of the protein tyrosine phosphatase YopH exhibit impaired WPD-loop function and crystallize with divanadate esters in their active sites.

G.Moise, N.M.Gallup, A.N.Alexandrova, A.C.Hengge, S.J.Johnson.

ABSTRACT

Catalysis in protein tyrosine phosphatases (PTPs) involves movement of a protein loop called the WPD loop that brings a conserved aspartic acid into the active site to function as a general acid. Mutation of the tryptophan in the WPD loop of the PTP YopH to any other residue with a planar, aromatic side chain (phenylalanine, tyrosine, or histidine) disables general acid catalysis. Crystal structures reveal these conservative mutations leave this critical loop in a catalytically unproductive, quasi-open position. Although the loop positions in crystal structures are similar for all three conservative mutants, the reasons inhibiting normal loop closure differ for each mutant. In the W354F and W354Y mutants, steric clashes result from six-membered rings occupying the position of the five-membered ring of the native indole side chain. The histidine mutant dysfunction results from new hydrogen bonds stabilizing the unproductive position. The results demonstrate how even modest modifications can disrupt catalytically important protein dynamics. Crystallization of all the catalytically compromised mutants in the presence of vanadate gave rise to vanadate dimers at the active site. In W354Y and W354H, a divanadate ester with glycerol is observed. Such species have precedence in solution and are known from the small molecule crystal database. Such species have not been observed in the active site of a phosphatase, as a functional phosphatase would rapidly catalyze their decomposition. The compromised functionality of the mutants allows the trapping of species that undoubtedly form in solution and are capable of binding at the active sites of PTPs, and, presumably, other phosphatases. In addition to monomeric vanadate, such higher-order vanadium-based molecules are likely involved in the interaction of vanadate with PTPs in solution.