PDBsum entry 1d1q

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Hydrolase PDB id
Protein chains
159 a.a. *
Waters ×368
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a yeast low molecular weight protein ty phosphatase (ltp1) complexed with the substrate pnpp
Structure: Tyrosine phosphatase chain: a, b. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.70Å     R-factor:   0.170     R-free:   0.215
Authors: S.Wang,L.Tabernero,M.Zhang,E.Harms,R.L.Van Etten,C.V.Staufac
Key ref:
S.Wang et al. (2000). Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate. Biochemistry, 39, 1903-1914. PubMed id: 10684639 DOI: 10.1021/bi991348d
20-Sep-99     Release date:   08-Mar-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P40347  (PPAL_YEAST) -  Low molecular weight phosphotyrosine protein phosphatase
161 a.a.
159 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
Bound ligand (Het Group name = 4NP)
matches with 45.83% similarity
+ 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/bi991348d Biochemistry 39:1903-1914 (2000)
PubMed id: 10684639  
Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.
S.Wang, L.Tabernero, M.Zhang, E.Harms, R.L.Van Etten, C.V.Stauffacher.
Low-molecular weight protein tyrosine phosphatases are virtually ubiquitous, which implies that they have important cellular functions. We present here the 2.2 A resolution X-ray crystallographic structure of wild-type LTP1, a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae. We also present the structure of an inactive mutant substrate complex of LTP1 with p-nitrophenyl phosphate (pNPP) at a resolution of 1.7 A. The crystal structures of the wild-type protein and of the inactive mutant both have two molecules per asymmetric unit. The wild-type protein crystal was grown in HEPES buffer, a sulfonate anion that resembles the phosphate substrate, and a HEPES molecule was found with nearly full occupancy in the active site. Although the fold of LTP1 resembles that of its bovine counterpart BPTP, there are significant changes around the active site that explain differences in their kinetic behavior. In the crystal of the inactive mutant of LTP1, one molecule has a pNPP in the active site, while the other has a phosphate ion. The aromatic residues lining the walls of the active site cavity exhibit large relative movements between the two molecules. The phosphate groups present in the structures of the mutant protein bind more deeply in the active site (that is, closer to the position of nucleophilic cysteine side chain) than does the sulfonate group of the HEPES molecule in the wild-type structure. This further confirms the important role of the phosphate-binding loop in stabilizing the deep binding position of the phosphate group, thus helping to bring the phosphate close to the thiolate anion of nucleophilic cysteine, and facilitating the formation of the phosphoenzyme intermediate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19616007 G.Hagelueken, H.Huang, I.L.Mainprize, C.Whitfield, and J.H.Naismith (2009).
Crystal structures of Wzb of Escherichia coli and CpsB of Streptococcus pneumoniae, representatives of two families of tyrosine phosphatases that regulate capsule assembly.
  J Mol Biol, 392, 678-688.
PDB codes: 2wja 2wjd 2wje 2wjf
19140798 T.A.Brandão, H.Robinson, S.J.Johnson, and A.C.Hengge (2009).
Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures.
  J Am Chem Soc, 131, 778-786.
PDB codes: 3f99 3f9a 3f9b
17975835 C.Madhurantakam, V.R.Chavali, and A.K.Das (2008).
Analyzing the catalytic mechanism of MPtpA: a low molecular weight protein tyrosine phosphatase from Mycobacterium tuberculosis through site-directed mutagenesis.
  Proteins, 71, 706-714.  
18298793 L.Tabernero, A.R.Aricescu, E.Y.Jones, and S.E.Szedlacsek (2008).
Protein tyrosine phosphatases: structure-function relationships.
  FEBS J, 275, 867-882.  
17154432 A.K.Hirsch, F.R.Fischer, and F.Diederich (2007).
Phosphate recognition in structural biology.
  Angew Chem Int Ed Engl, 46, 338-352.  
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
16651264 E.Lescop, Y.Hu, H.Xu, W.Hu, J.Chen, B.Xia, and C.Jin (2006).
The solution structure of Escherichia coli Wzb reveals a novel substrate recognition mechanism of prokaryotic low molecular weight protein-tyrosine phosphatases.
  J Biol Chem, 281, 19570-19577.
PDB code: 2fek
16452434 H.Xu, B.Xia, and C.Jin (2006).
Solution structure of a low-molecular-weight protein tyrosine phosphatase from Bacillus subtilis.
  J Bacteriol, 188, 1509-1517.
PDB code: 1zgg
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
15743966 C.Madhurantakam, E.Rajakumara, P.A.Mazumdar, B.Saha, D.Mitra, H.G.Wiker, R.Sankaranarayanan, and A.K.Das (2005).
Crystal structure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-A resolution.
  J Bacteriol, 187, 2175-2181.
PDB codes: 1u2p 1u2q
15234974 L.Tao, and A.L.Harris (2004).
Biochemical requirements for inhibition of Connexin26-containing channels by natural and synthetic taurine analogs.
  J Biol Chem, 279, 38544-38554.  
15373838 R.Krumscheid, R.Ettrich, Z.Sovová, K.Susánková, Z.Lánský, K.Hofbauerová, H.Linnertz, J.Teisinger, E.Amler, and W.Schoner (2004).
The phosphatase activity of the isolated H4-H5 loop of Na+/K+ ATPase resides outside its ATP binding site.
  Eur J Biochem, 271, 3923-3936.  
12606538 A.Meinhart, T.Silberzahn, and P.Cramer (2003).
The mRNA transcription/processing factor Ssu72 is a potential tyrosine phosphatase.
  J Biol Chem, 278, 15917-15921.  
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.  
11805096 D.F.McCain, I.E.Catrina, A.C.Hengge, and Z.Y.Zhang (2002).
The catalytic mechanism of Cdc25A phosphatase.
  J Biol Chem, 277, 11190-11200.  
11971972 E.K.Park, N.Warner, K.Mood, T.Pawson, and I.O.Daar (2002).
Low-molecular-weight protein tyrosine phosphatase is a positive component of the fibroblast growth factor receptor signaling pathway.
  Mol Cell Biol, 22, 3404-3414.  
  11408586 N.Alic, V.J.Higgins, and I.W.Dawes (2001).
Identification of a Saccharomyces cerevisiae gene that is required for G1 arrest in response to the lipid oxidation product linoleic acid hydroperoxide.
  Mol Biol Cell, 12, 1801-1810.  
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 codes are shown on the right.