PDBsum entry 1d2a

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
156 a.a. *
PO4 ×2
Waters ×300
* Residue conservation analysis
PDB id:
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)
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+
22-Sep-99     Release date:   01-Mar-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P40347  (PPAL_YEAST) -  Low molecular weight phosphotyrosine protein phosphatase
161 a.a.
156 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.  - Acid phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphate monoester + H2O = an alcohol + phosphate
phosphate monoester
+ H(2)O
= alcohol
Bound ligand (Het Group name = PO4)
corresponds exactly
   Enzyme class 3: E.C.  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
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 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     peptidyl-tyrosine dephosphorylation   2 terms 
  Biochemical function     hydrolase activity     4 terms  


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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19678837 J.Blobel, P.Bernadó, H.Xu, C.Jin, and M.Pons (2009).
Weak oligomerization of low-molecular-weight protein tyrosine phosphatase is conserved from mammals to bacteria.
  FEBS J, 276, 4346-4357.  
17543532 R.Maccari, P.Paoli, R.Ottanà, M.Jacomelli, R.Ciurleo, G.Manao, T.Steindl, T.Langer, M.G.Vigorita, and G.Camici (2007).
5-Arylidene-2,4-thiazolidinediones as inhibitors of protein tyrosine phosphatases.
  Bioorg Med Chem, 15, 5137-5149.  
16253994 A.P.Zabell, A.D.Schroff, B.E.Bain, R.L.Van Etten, O.Wiest, and C.V.Stauffacher (2006).
Crystal structure of the human B-form low molecular weight phosphotyrosyl phosphatase at 1.6-A resolution.
  J Biol Chem, 281, 6520-6527.
PDB code: 1xww
17008719 D.Tolkatchev, R.Shaykhutdinov, P.Xu, J.Plamondon, D.C.Watson, N.M.Young, and F.Ni (2006).
Three-dimensional structure and ligand interactions of the low molecular weight protein tyrosine phosphatase from Campylobacter jejuni.
  Protein Sci, 15, 2381-2394.
PDB code: 2gi4
16195543 C.L.Gustafson, C.V.Stauffacher, K.Hallenga, and R.L.Van Etten (2005).
Solution structure of the low-molecular-weight protein tyrosine phosphatase from Tritrichomonas foetus reveals a flexible phosphate binding loop.
  Protein Sci, 14, 2515-2525.
PDB code: 1p8a
12660165 C.Ganem, F.Devaux, C.Torchet, C.Jacq, S.Quevillon-Cheruel, G.Labesse, C.Facca, and G.Faye (2003).
Ssu72 is a phosphatase essential for transcription termination of snoRNAs and specific mRNAs in yeast.
  EMBO J, 22, 1588-1598.  
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 code is shown on the right.