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Catalytic Site Atlas

CSA LITERATURE entry for 1pa9

E.C. nameprotein-tyrosine-phosphatase
SpeciesYersinia enterocolitica (Bacteria)
E.C. Number (IntEnz) 3.1.3.48
CSA Homologues of 1pa9
CSA Entries With UniProtID P15273
CSA Entries With EC Number 3.1.3.48
PDBe Entry 1pa9
PDBSum Entry 1pa9
MACiE Entry M0047

Literature Report

IntroductionThe Yersinia genus contains a plasmid encoding a virulence factor, YopH, a tyrosine phosphatase which translocates itself into the host cell using the N-terminus. The catalytic domains are structurally homologous to human PTP1B, which is also a tyrosine phosphatase. YopH cleaves the phosphate off phosphorylated tyrosine residues on host proteins, interrupting the control of many eukaryotic cellular processes, and contributes to the ability to resist phagocytosis by peritoneal macrophages.
MechansimThe mechanism is thought to be primarily dissociative, with more catalytic importance placed on stabilising the negative charge on the leaving group, rather than activation of the nucleophile. Phosphoryl transfer occurs in a single step, with an inline displacement mechanism.
1) Thr 410 hydrogen bonds to Cys 403, lowering Cys 403's pKa and stabilising a thiolate anion on this residue.
2) Asp 356 is protonated, and acts as a general acid to protonate the substrate tyrosine residue, promoting phosphoryl transfer.
3) The trigonal bipyramid transition state is stabilised by Arg 409.
4) Cys 403 becomes phosphorylated. The substrate is released and water enters the active site.
5) Asp 356 activates the water molecule by hydrogen bonding.
6) During phosphoryl transfer, Thr 410 stabilises the growing negative charge on the thiolate of Cys 403. Arg 409 again stabilises the transition state. Asp 356 deprotonates the water nucleophile.
7) Inorganic phosphate is formed.
Reaction

Catalytic Sites for 1pa9

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ThrA248410macie:sideChainThr 410 lowers the pKa of the nucleophilic Cys 403, and stabilises the thiolate anion as a leaving group during phosphoenzyme hydrolysis.
CysA241403macie:sideChainCys 403 is nucleophilic, removing the phosphoryl group from the substrate.
ArgA247409macie:sideChainArg 409 stabilises the transition states, through coplanar, divalent guanidium-phosphate interactions.
AspA194356macie:sideChainAsp 356 acts as an general acid-base catalyst, protonating the substrate and deprotonating the nucleophilic water molecule.

Literature References

Notes:
Guan KL
Evidence for protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate.
J Biol Chem 1991 266 17026-17030
PubMed: 1654322
Pannifer AD
Visualization of the cysteinyl-phosphate intermediate of a protein-tyrosine phosphatase by x-ray crystallography.
J Biol Chem 1998 273 10454-10462
PubMed: 9553104
Stuckey JA
Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate.
Nature 1994 370 571-575
PubMed: 8052312
Zhang ZY
Dissecting the catalytic mechanism of protein-tyrosine phosphatases.
Proc Natl Acad Sci U S A 1994 91 1624-1627
PubMed: 8127855
Zhang ZY
The Cys(X)5Arg catalytic motif in phosphoester hydrolysis.
Biochemistry 1994 33 15266-15270
PubMed: 7803389
Zhang ZY
Catalytic function of the conserved hydroxyl group in the protein tyrosine phosphatase signature motif.
Biochemistry 1995 34 16389-16396
PubMed: 8845365
Zhang ZY.
Mechanistic studies on protein tyrosine phosphatases.
Prog Nucleic Acid Res Mol Biol 2003 73 171-220
PubMed: 12882518
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