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Catalytic Site Atlas

CSA LITERATURE entry for 1d1q

E.C. nameacid phosphatase
SpeciesSaccharomyces cerevisiae (Baker's yeast)
E.C. Number (IntEnz) 3.1.3.2
CSA Homologues of 1d1q
CSA Entries With UniProtID P40347
CSA Entries With EC Number 3.1.3.2
PDBe Entry 1d1q
PDBSum Entry 1d1q
MACiE Entry 1d1q

Literature Report

IntroductionLTP1 is a low molecular weight tyrosine phosphatase from Saccharomyces cerevisiae. As part of the PTPase superfamily, it shows little sequence similarity to other tyrosine phosphatases, but retains the conserved catalytic components, in particular the CXXXXXRS/T 'P loop'. The mechanism is therefore thought to be the same as that of the rest of the superfamily.
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) Ser 20 hydrogen bonds to Cys 13, lowering Cys 13's pKa and stabilising a thiolate anion on this residue.
2) Asp 132 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 19.
4) Cys 13 becomes phosphorylated. The substrate is released and water enters the active site.
5) Asp 132 activates the water molecule by hydrogen bonding.
6) During phosphoryl transfer, Ser 20 stabilises the growing negative charge on the thiolate of Cys 13. Arg 19 again stabilises the transition state.
7) Inorganic phosphate is formed, with Asp 132 deprotonating the nucleophilic water to regenerate its protonated state.
There is computational evidence that suggests that, for low molecular weight PTPs, Cys 13 is protonated in the ground state, and transfers its proton to the phosphoryl group (i.e. substrate assisted catalysis) before nucleophilic attack.
Reaction

Catalytic Sites for 1d1q

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AlaA1314macie:sideChainCys 13 is the nucleophilic active site residue that displaces the substrate from the phosphoryl group, becoming phosphorylated itself.
ArgA1920macie:sideChainStabilises the transition states specifically, via a bidentate guanidinium-phosphoryl interaction.
SerA2021macie:sideChainThe hydroxyl group of Ser 20 lowers the pKa of Cys 13, making it more nucleophilic.
Ser 20 stabilises the thiolate anion as a leaving group in the phosphoenzyme hydrolysis step.
AspA132133macie:sideChainActs as the acid-base catalyst, protonating the substrate to encourage phosphoryl dissociation, and deprotonating the water nucleophile.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AlaB1314macie:sideChainCys 13 is the nucleophilic active site residue that displaces the substrate from the phosphoryl group, becoming phosphorylated itself.
ArgB1920macie:sideChainStabilises the transition states specifically, via a bidentate guanidinium-phosphoryl interaction.
SerB2021macie:sideChainThe hydroxyl group of Ser 20 lowers the pKa of Cys 13, making it more nucleophilic.
Ser 20 stabilises the thiolate anion as a leaving group in the phosphoenzyme hydrolysis step.
AspB132133macie:sideChainActs as the acid-base catalyst, protonating the substrate to encourage phosphoryl dissociation, and deprotonating the water nucleophile.

Literature References

Notes:See also CSA entries 1PA9 and 1BZC (Yersinia and human PTPases) for further evidence, as most research has been on that branch of the PTPase superfamily.
Wang S
Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.
Biochemistry 2000 39 1903-1914
PubMed: 10684639
Zhang ZY.
Mechanistic studies on protein tyrosine phosphatases.
Prog Nucleic Acid Res Mol Biol 2003 73 171-220
PubMed: 12882518
Kolmodin K
Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase.
Proteins 1999 36 370-379
PubMed: 10409830
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