PDBsum entry: 1d2a

Hydrolase

PDB id: 1d2a

Contents

Protein chains

156 a.a. *

Ligands

PO4 ×2

ADE

Metals

_CL

Waters ×300

* Residue conservation analysis

PDB id:

1d2a

Name:

Hydrolase

Title:

Crystal structure of a yeast low molecular weight protein tyrosine phosphatase (ltp1) complexed with the activator adenine

Structure:

Tyrosine phosphatase. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: inactive mutant of ltp1 that the nucleophile cysteine is mutated to alanine is used.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.182 R-free: 0.243

Authors:

S.Wang,C.V.Stauffacher,R.L.Van Etten

Key ref:

S.Wang et al. (2000). Structural and mechanistic basis for the activation of a low-molecular weight protein tyrosine phosphatase by adenine. Biochemistry, 39, 1234-1242. PubMed id: 10684601 DOI: 10.1021/bi991515+

Date:

22-Sep-99 Release date: 01-Mar-00

Protein chains

P40347  (PPAL_YEAST) -  Low molecular weight phosphotyrosine protein phosphatase

Seq: 161 a.a.

Struc: 156 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.3.1.3.2 - Acid phosphatase.
• Reaction: A phosphate monoester + H₂O = an alcohol + phosphate

phosphate monoester + H(2)O = alcohol + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 3: E.C.3.1.3.48 - Protein-tyrosine-phosphatase.
• Reaction: Protein tyrosine phosphate + H₂O = protein tyrosine + phosphate

Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (2 terms)
• Biological process: protein amino acid dephosphorylation (1 term)
• Biochemical function: protein binding (5 terms)

reference

DOI no: 10.1021/bi991515+

Biochemistry 39:1234-1242 (2000)

PubMed id: 10684601

Structural and mechanistic basis for the activation of a low-molecular weight protein tyrosine phosphatase by adenine.

S.Wang, C.V.Stauffacher, R.L.Van Etten.

ABSTRACT

Although the activation of low-molecular weight protein tyrosine phosphatases by certain purines and purine derivatives was first described three decades ago, the mechanism of this rate enhancement was unknown. As an example, adenine activates the yeast low-molecular weight protein tyrosine phosphatase LTP1 more than 30-fold. To examine the structural and mechanistic basis of this phenomenon, we have determined the crystal structure of yeast LTP1 complexed with adenine. In the crystal structure, an adenine molecule is found bound in the active site cavity, sandwiched between the side chains of two large hydrophobic residues at the active site. Hydrogen bonding to the side chains of other active site residues, as well as some water-mediated hydrogen bonds, also helps to fix the position of the bound adenine molecule. An ordered water was found in proximity to the bound phosphate ion present in the active site, held by hydrogen bonding to N3 of adenine and Odelta1 of Asp-132. On the basis of the crystal structure, we propose that this water molecule is the nucleophile that participates in the dephosphorylation of the phosphoenzyme intermediate. Solvent isotope effect studies show that there is no rate-determining transfer of a solvent-derived proton in the transition state for the dephosphorylation of the phosphoenzyme intermediate. Such an absence of general base catalysis of water attack is consistent with the stability of the leaving group, namely, the thiolate anion of Cys-13. Consequently, adenine activates the enzyme by binding and orienting a water nucleophile in proximity to the phosphoryl group of the phosphoenzyme intermediate, thus increasing the rate of the dephosphorylation step, a step that is normally the rate-limiting step of this enzymatic reaction.