PDBsum entry 1phr

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Phosphotyrosine protein phosphatase PDB id
Protein chain
154 a.a. *
Waters ×70
* Residue conservation analysis
PDB id:
Name: Phosphotyrosine protein phosphatase
Title: The crystal structure of a low molecular phosphotyrosine protein phosphatase
Structure: Low molecular weight phosphotyrosine protein phosphotase. Chain: a. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913
2.10Å     R-factor:   0.167     R-free:   0.232
Authors: X.-D.Su,N.Taddei,M.Stefani,G.Ramponi,P.Nordlund
Key ref: X.D.Su et al. (1994). The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase. Nature, 370, 575-578. PubMed id: 8052313
05-Jul-94     Release date:   31-Jul-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P11064  (PPAC_BOVIN) -  Low molecular weight phosphotyrosine protein phosphatase
158 a.a.
154 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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
+ phosphate
   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
+ phosphate
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     5 terms  


Nature 370:575-578 (1994)
PubMed id: 8052313  
The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase.
X.D.Su, N.Taddei, M.Stefani, G.Ramponi, P.Nordlund.
Protein tyrosine phosphorylation and dephosphorylation are central reactions for control of cellular division, differentiation and development. Here we describe the crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase (PTPase), a cytosolic phosphatase present in many mammalian cells. The enzyme catalyses the dephosphorylation of phosphotyrosine-containing substrates, and overexpression of the protein in normal and transformed cells inhibits cell proliferation. The structure of the low-molecular-weight PTPase reveals an alpha/beta protein containing a phosphate-binding loop motif at the amino end of helix alpha 1. This motif includes the essential active-site residues Cys 12 and Arg 18 and bears striking similarities to the active-site motif recently described in the structure of human PTP1B. The structure of the low-molecular-weight PTPase supports a reaction mechanism involving the conserved Cys 12 as an attacking nucleophile in an in-line associative mechanism. The structure also suggests a catalytic role for Asp 129 in the reaction cycle.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21258851 S.Jain, B.Saluja, A.Gupta, S.S.Marla, and R.Goel (2011).
Validation of Arsenic Resistance in Bacillus cereus Strain AG27 by Comparative Protein Modeling of arsC Gene Product.
  Protein J, 30, 91.  
20466768 J.C.Fong, K.A.Syed, K.E.Klose, and F.H.Yildiz (2010).
Role of Vibrio polysaccharide (vps) genes in VPS production, biofilm formation and Vibrio cholerae pathogenesis.
  Microbiology, 156, 2757-2769.  
20861839 K.Xiang, T.Nagaike, S.Xiang, T.Kilic, M.M.Beh, J.L.Manley, and L.Tong (2010).
Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex.
  Nature, 467, 729-733.
PDB codes: 3o2q 3o2s 3o2t 3odr 3ods
19489729 A.Edwards (2009).
Large-scale structural biology of the human proteome.
  Annu Rev Biochem, 78, 541-568.  
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.  
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
15890001 A.Salmeen, and D.Barford (2005).
Functions and mechanisms of redox regulation of cysteine-based phosphatases.
  Antioxid Redox Signal, 7, 560-577.  
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
15654077 C.Tang, D.C.Williams, R.Ghirlando, and G.M.Clore (2005).
Solution structure of enzyme IIA(Chitobiose) from the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.
  J Biol Chem, 280, 11770-11780.
PDB code: 1wcr
15611135 F.Villa, M.Deak, G.B.Bloomberg, D.R.Alessi, and D.M.van Aalten (2005).
Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket.
  J Biol Chem, 280, 8180-8187.
PDB code: 1wch
15670209 K.Hamada, M.Kato, T.Shimizu, K.Ihara, T.Mizuno, and T.Hakoshima (2005).
Crystal structure of the protein histidine phosphatase SixA in the multistep His-Asp phosphorelay.
  Genes Cells, 10, 1.
PDB codes: 1ujb 1ujc
16080154 K.Miyazono, Y.Sawano, and M.Tanokura (2005).
Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Proteins, 61, 196-205.  
15900534 L.Bialy, and H.Waldmann (2005).
Inhibitors of protein tyrosine phosphatases: next-generation drugs?
  Angew Chem Int Ed Engl, 44, 3814-3839.  
16192272 X.Guo, Y.Li, K.Peng, Y.Hu, C.Li, B.Xia, and C.Jin (2005).
Solution structures and backbone dynamics of arsenate reductase from Bacillus subtilis: reversible conformational switch associated with arsenate reduction.
  J Biol Chem, 280, 39601-39608.
PDB codes: 1z2d 1z2e
15159594 J.Messens, I.Van Molle, P.Vanhaesebrouck, K.Van Belle, K.Wahni, J.C.Martins, L.Wyns, and R.Loris (2004).
The structure of a triple mutant of pI258 arsenate reductase from Staphylococcus aureus and its 5-thio-2-nitrobenzoic acid adduct.
  Acta Crystallogr D Biol Crystallogr, 60, 1180-1184.
PDB codes: 1rxe 1rxi
15258141 P.M.Legler, M.Cai, A.Peterkofsky, and G.M.Clore (2004).
Three-dimensional solution structure of the cytoplasmic B domain of the mannitol transporter IImannitol of the Escherichia coli phosphotransferase system.
  J Biol Chem, 279, 39115-39121.
PDB code: 1vkr
15159593 S.Zuccotti, C.Rosano, M.Ramazzotti, D.Degl'Innocenti, M.Stefani, G.Manao, and M.Bolognesi (2004).
Three-dimensional structural characterization of a novel Drosophila melanogaster acylphosphatase.
  Acta Crystallogr D Biol Crystallogr, 60, 1177-1179.
PDB code: 1urr
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.  
12657060 G.Klein, C.Dartigalongue, and S.Raina (2003).
Phosphorylation-mediated regulation of heat shock response in Escherichia coli.
  Mol Microbiol, 48, 269-285.  
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.  
12145214 M.Selmer, and X.D.Su (2002).
Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.
  EMBO J, 21, 4145-4153.
PDB code: 1lva
11976341 N.Bottini, L.Stefanini, S.Williams, A.Alonso, T.Jascur, R.T.Abraham, C.Couture, and T.Mustelin (2002).
Activation of ZAP-70 through specific dephosphorylation at the inhibitory Tyr-292 by the low molecular weight phosphotyrosine phosphatase (LMPTP).
  J Biol Chem, 277, 24220-24224.  
11350947 A.Changela, C.K.Ho, A.Martins, S.Shuman, and A.Mondragón (2001).
Structure and mechanism of the RNA triphosphatase component of mammalian mRNA capping enzyme.
  EMBO J, 20, 2575-2586.
PDB codes: 1i9s 1i9t
11258771 A.Modesti, L.Bini, L.Carraresi, F.Magherini, S.Liberatori, V.Pallini, G.Manao, L.A.Pinna, G.Raugei, and G.Ramponi (2001).
Expression of the small tyrosine phosphatase (Stp1) in Saccharomyces cerevisiae: a study on protein tyrosine phosphorylation.
  Electrophoresis, 22, 576-585.  
11698660 M.S.Bennett, Z.Guan, M.Laurberg, and X.D.Su (2001).
Bacillus subtilis arsenate reductase is structurally and functionally similar to low molecular weight protein tyrosine phosphatases.
  Proc Natl Acad Sci U S A, 98, 13577-13582.
PDB code: 1jl3
11709171 P.Martin, S.DeMel, J.Shi, T.Gladysheva, D.L.Gatti, B.P.Rosen, and B.F.Edwards (2001).
Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme.
  Structure, 9, 1071-1081.
PDB codes: 1i9d 1j9b 1jzw
  11574689 V.G.Metelev, O.A.Borisova, E.M.Volkov, T.S.Oretskaya, and N.G.Dolinnaya (2001).
New chemically reactive dsDNAs containing single internucleotide monophosphoryldithio links: reactivity of 5'-mercapto-oligodeoxyribonucleotides.
  Nucleic Acids Res, 29, 4062-4069.  
10698923 M.Worbs, R.Huber, and M.C.Wahl (2000).
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
  EMBO J, 19, 807-818.
PDB code: 1dmg
10469598 E.Emmanouilidou, A.G.Teschemacher, A.E.Pouli, L.I.Nicholls, E.P.Seward, and G.A.Rutter (1999).
Imaging Ca2+ concentration changes at the secretory vesicle surface with a recombinant targeted cameleon.
  Curr Biol, 9, 915-918.  
10393270 G.T.Robillard, and J.Broos (1999).
Structure/function studies on the bacterial carbohydrate transporters, enzymes II, of the phosphoenolpyruvate-dependent phosphotransferase system.
  Biochim Biophys Acta, 1422, 73.  
10491176 H.Schüler, E.Korenbaum, C.E.Schutt, U.Lindberg, and R.Karlsson (1999).
Mutational analysis of Ser14 and Asp157 in the nucleotide-binding site of beta-actin.
  Eur J Biochem, 265, 210-220.  
10409830 K.Kolmodin, P.Nordlund, and J.Aqvist (1999).
Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase.
  Proteins, 36, 370-379.  
10369665 O.Ilan, Y.Bloch, G.Frankel, H.Ullrich, K.Geider, and I.Rosenshine (1999).
Protein tyrosine kinases in bacterial pathogens are associated with virulence and production of exopolysaccharide.
  EMBO J, 18, 3241-3248.  
10336608 P.Tailor, J.Gilman, S.Williams, and T.Mustelin (1999).
A novel isoform of the low molecular weight phosphotyrosine phosphatase, LMPTP-C, arising from alternative mRNA splicing.
  Eur J Biochem, 262, 277-282.  
9829991 A.Caselli, R.Marzocchini, G.Camici, G.Manao, G.Moneti, G.Pieraccini, and G.Ramponi (1998).
The inactivation mechanism of low molecular weight phosphotyrosine-protein phosphatase by H2O2.
  J Biol Chem, 273, 32554-32560.  
  9841674 G.R.Cornelis, A.Boland, A.P.Boyd, C.Geuijen, M.Iriarte, C.Neyt, M.P.Sory, and I.Stainier (1998).
The virulence plasmid of Yersinia, an antihost genome.
  Microbiol Mol Biol Rev, 62, 1315-1352.  
9818190 J.M.Denu, and J.E.Dixon (1998).
Protein tyrosine phosphatases: mechanisms of catalysis and regulation.
  Curr Opin Chem Biol, 2, 633-641.  
9774441 J.Yang, X.Liang, T.Niu, W.Meng, Z.Zhao, and G.W.Zhou (1998).
Crystal structure of the catalytic domain of protein-tyrosine phosphatase SHP-1.
  J Biol Chem, 273, 28199-28207.
PDB code: 1gwz
9835619 M.Parola, G.Robino, F.Marra, M.Pinzani, G.Bellomo, G.Leonarduzzi, P.Chiarugi, S.Camandola, G.Poli, G.Waeg, P.Gentilini, and M.U.Dianzani (1998).
HNE interacts directly with JNK isoforms in human hepatic stellate cells.
  J Clin Invest, 102, 1942-1950.  
9705307 M.Zhang, C.V.Stauffacher, D.Lin, and R.L.Van Etten (1998).
Crystal structure of a human low molecular weight phosphotyrosyl phosphatase. Implications for substrate specificity.
  J Biol Chem, 273, 21714-21720.
PDB code: 5pnt
9506979 P.Chiarugi, P.Cirri, F.Marra, G.Raugei, T.Fiaschi, G.Camici, G.Manao, R.G.Romanelli, and G.Ramponi (1998).
The Src and signal transducers and activators of transcription pathways as specific targets for low molecular weight phosphotyrosine-protein phosphatase in platelet-derived growth factor signaling.
  J Biol Chem, 273, 6776-6785.  
9624118 S.R.Lee, K.S.Kwon, S.R.Kim, and S.G.Rhee (1998).
Reversible inactivation of protein-tyrosine phosphatase 1B in A431 cells stimulated with epidermal growth factor.
  J Biol Chem, 273, 15366-15372.  
9817026 T.R.Burke, and Z.Y.Zhang (1998).
Protein-tyrosine phosphatases: structure, mechanism, and inhibitor discovery.
  Biopolymers, 47, 225-241.  
9488671 Y.Zhao, L.Wu, S.J.Noh, K.L.Guan, and Z.Y.Zhang (1998).
Altering the nucleophile specificity of a protein-tyrosine phosphatase-catalyzed reaction. Probing the function of the invariant glutamine residues.
  J Biol Chem, 273, 5484-5492.  
  9041631 E.Ab, G.Schuurman-Wolters, J.Reizer, M.H.Saier, K.Dijkstra, R.M.Scheek, and G.T.Robillard (1997).
The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli.
  Protein Sci, 6, 304-314.
PDB code: 1e2b
9141461 G.Draetta, and J.Eckstein (1997).
Cdc25 protein phosphatases in cell proliferation.
  Biochim Biophys Acta, 1332, M53-M63.  
9147129 G.Ramponi, and M.Stefani (1997).
Structural, catalytic, and functional properties of low M(r), phosphotyrosine protein phosphatases. Evidence of a long evolutionary history.
  Int J Biochem Cell Biol, 29, 279-292.  
9016712 M.M.Thunnissen, N.Taddei, G.Liguri, G.Ramponi, and P.Nordlund (1997).
Crystal structure of common type acylphosphatase from bovine testis.
  Structure, 5, 69-79.
PDB code: 2acy
9038134 P.Tailor, J.Gilman, S.Williams, C.Couture, and T.Mustelin (1997).
Regulation of the low molecular weight phosphotyrosine phosphatase by phosphorylation at tyrosines 131 and 132.
  J Biol Chem, 272, 5371-5374.  
9032081 R.L.van Montfort, T.Pijning, K.H.Kalk, J.Reizer, M.H.Saier, M.M.Thunnissen, G.T.Robillard, and B.W.Dijkstra (1997).
The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases.
  Structure, 5, 217-225.
PDB code: 1iib
  9003755 A.K.Das, N.R.Helps, P.T.Cohen, and D.Barford (1996).
Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution.
  EMBO J, 15, 6798-6809.
PDB code: 1a6q
8987394 E.B.Fauman, and M.A.Saper (1996).
Structure and function of the protein tyrosine phosphatases.
  Trends Biochem Sci, 21, 413-417.  
  8845750 E.S.Muise, A.Vrielink, M.A.Ennis, N.H.Lemieux, and M.L.Tremblay (1996).
Thermosensitive mutants of the MPTP and hPTP1B protein tyrosine phosphatases: isolation and structural analysis.
  Protein Sci, 5, 604-613.  
8898189 J.M.Denu, J.A.Stuckey, M.A.Saper, and J.E.Dixon (1996).
Form and function in protein dephosphorylation.
  Cell, 87, 361-364.  
  8771191 J.W.Eckstein, P.Beer-Romero, and I.Berdo (1996).
Identification of an essential acidic residue in Cdc25 protein phosphatase and a general three-dimensional model for a core region in protein phosphatases.
  Protein Sci, 5, 5.  
8805550 Madhusudan, J.Zapf, J.M.Whiteley, J.A.Hoch, N.H.Xuong, and K.I.Varughese (1996).
Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis.
  Structure, 4, 679-690.
PDB code: 1srr
8576112 S.Rigacci, D.Degl'Innocenti, M.Bucciantini, P.Cirri, A.Berti, and G.Ramponi (1996).
pp60v-src phosphorylates and activates low molecular weight phosphotyrosine-protein phosphatase.
  J Biol Chem, 271, 1278-1281.  
8900062 T.Umeyama, Y.Tanabe, B.D.Aigle, and S.Horinouchi (1996).
Expression of the Streptomyces coelicolor A3(2) ptpA gene encoding a phosphotyrosine protein phosphatase leads to overproduction of secondary metabolites in S. lividans.
  FEMS Microbiol Lett, 144, 177-184.  
8617791 X.Xu, and S.P.Burke (1996).
Roles of active site residues and the NH2-terminal domain in the catalysis and substrate binding of human Cdc25.
  J Biol Chem, 271, 5118-5124.  
7876123 C.Pokalsky, P.Wick, E.Harms, F.E.Lytle, and R.L.Van Etten (1995).
Fluorescence resolution of the intrinsic tryptophan residues of bovine protein tyrosyl phosphatase.
  J Biol Chem, 270, 3809-3815.  
8846213 D.Barford, Z.Jia, and N.K.Tonks (1995).
Protein tyrosine phosphatases take off.
  Nat Struct Biol, 2, 1043-1053.  
8749359 D.Barford (1995).
Protein phosphatases.
  Curr Opin Struct Biol, 5, 728-734.  
8522318 E.Bottini, F.Gloria-Bottini, and P.Borgiani (1995).
ACP1 and human adaptability. 1. Association with common diseases: a case-control study.
  Hum Genet, 96, 629-637.  
  8528087 H.L.Schubert, E.B.Fauman, J.A.Stuckey, J.E.Dixon, and M.A.Saper (1995).
A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase.
  Protein Sci, 4, 1904-1913.
PDB code: 1yts
7476194 J.Huang, and M.Schell (1995).
Molecular characterization of the eps gene cluster of Pseudomonas solanacearum and its transcriptional regulation at a single promoter.
  Mol Microbiol, 16, 977-989.  
7597052 J.M.Denu, and J.E.Dixon (1995).
A catalytic mechanism for the dual-specific phosphatases.
  Proc Natl Acad Sci U S A, 92, 5910-5914.  
8569721 K.Balendiran, Y.Tan, R.K.Sharma, and K.H.Murthy (1995).
Preliminary crystallization studies of calmodulin-dependent protein phosphatase (calcineurin) from bovine brain.
  Mol Cell Biochem, 149, 127-130.  
7629177 K.Ostanin, C.Pokalsky, S.Wang, and R.L.Van Etten (1995).
Cloning and characterization of a Saccharomyces cerevisiae gene encoding the low molecular weight protein-tyrosine phosphatase.
  J Biol Chem, 270, 18491-18499.  
7596293 P.Bugert, and K.Geider (1995).
Molecular analysis of the ams operon required for exopolysaccharide synthesis of Erwinia amylovora.
  Mol Microbiol, 15, 917-933.  
  7537849 T.A.Gustafson, W.He, A.Craparo, C.D.Schaub, and T.J.O'Neill (1995).
Phosphotyrosine-dependent interaction of SHC and insulin receptor substrate 1 with the NPEY motif of the insulin receptor via a novel non-SH2 domain.
  Mol Cell Biol, 15, 2500-2508.  
8578591 Z.Songyang, and L.C.Cantley (1995).
Recognition and specificity in protein tyrosine kinase-mediated signalling.
  Trends Biochem Sci, 20, 470-475.  
7529177 J.Wagner, D.Boerboom, and M.L.Tremblay (1994).
Molecular cloning and tissue-specific RNA processing of a murine receptor-type protein tyrosine phosphatase.
  Eur J Biochem, 226, 773-782.  
8001547 Y.Sakakibara, M.Suiko, and M.C.Liu (1994).
De novo sulfation of L-tyrosine in HepG2 human hepatoma cells and its possible functional implication.
  Eur J Biochem, 226, 293-301.  
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.