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PDBsum entry 1pnt

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Hydrolase PDB id
1pnt
Jmol
Contents
Protein chain
157 a.a. *
Ligands
PO4
* Residue conservation analysis
PDB id:
1pnt
Name: Hydrolase
Title: Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2 angstroms resolution
Structure: Acid phosphatase. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
2.20Å     R-factor:   0.166    
Authors: M.Zhang,R.L.Van Etten,C.V.Stauffacher
Key ref:
M.Zhang et al. (1994). Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2-A resolution. Biochemistry, 33, 11097-11105. PubMed id: 7537084 DOI: 10.1021/bi00203a006
Date:
05-Aug-94     Release date:   07-Feb-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class 2: E.C.3.1.3.2  - Acid phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      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.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      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 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     peptidyl-tyrosine dephosphorylation   2 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00203a006 Biochemistry 33:11097-11105 (1994)
PubMed id: 7537084  
 
 
Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2-A resolution.
M.Zhang, R.L.Van Etten, C.V.Stauffacher.
 
  ABSTRACT  
 
The first X-ray crystallographic structure of a member of the class of low molecular weight (M(r) 18,000) phosphotyrosyl phosphatases is presented. Bovine heart phosphotyrosyl phosphatase (BHPTP) exemplifies this class and is highly homologous (94% sequence identity) to an isoenzyme known as red cell acid phosphatase that is present throughout human tissues. The high-resolution (2.2-A) crystal structure of BHPTP shows that the enzyme consists of a four-strand central parallel beta sheet with alpha helices packed on both sides in a manner characteristic of a Rossmann fold. A bound phosphate ion defines the active site location in a loop of the first beta alpha beta motif at the C-terminus of the beta sheet. The location and enzymatic significance of the residues in the characteristic low molecular weight PTPase active site motif, including the essential arginine (Arg 18) and nucleophilic cysteine (Cys 12), are described. The functional role of a histidine (His 72) suggested previously to be near the active site is defined in the structure, as well as a potential proton donor for the leaving group in the tyrosyl phosphate cleavage. Surface maps of BHPTP define a hydrophobic crevice suitable for phosphotyrosyl peptide binding. Comparison of the BHPTP structure to the related, but structurally distinct enzyme PTP1B is made, illustrating the unique way this smallest of these phosphatases has formed the phosphotyrosine active site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19959833 Y.S.Jung, M.Cai, and G.M.Clore (2010).
Solution structure of the IIAChitobiose-IIBChitobiose complex of the N,N'-diacetylchitobiose branch of the Escherichia coli phosphotransferase system.
  J Biol Chem, 285, 4173-4184.
PDB codes: 2wwv 2wy2
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.  
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.  
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
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
16100107 K.E.Christensen, I.A.Mirza, A.M.Berghuis, and R.E.Mackenzie (2005).
Magnesium and phosphate ions enable NAD binding to methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase.
  J Biol Chem, 280, 34316-34323.
PDB code: 1zn4
14716003 M.Garcia-Viloca, J.Gao, M.Karplus, and D.G.Truhlar (2004).
How enzymes work: analysis by modern rate theory and computer simulations.
  Science, 303, 186-195.  
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
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.  
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
10409830 K.Kolmodin, P.Nordlund, and J.Aqvist (1999).
Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase.
  Proteins, 36, 370-379.  
9685474 C.C.Zhang, L.Gonzalez, and V.Phalip (1998).
Survey, analysis and genetic organization of genes encoding eukaryotic-like signaling proteins on a cyanobacterial genome.
  Nucleic Acids Res, 26, 3619-3625.  
  9499402 E.Stein, A.A.Lane, D.P.Cerretti, H.O.Schoecklmann, A.D.Schroff, R.L.Van Etten, and T.O.Daniel (1998).
Eph receptors discriminate specific ligand oligomers to determine alternative signaling complexes, attachment, and assembly responses.
  Genes Dev, 12, 667-678.  
9818190 J.M.Denu, and J.E.Dixon (1998).
Protein tyrosine phosphatases: mechanisms of catalysis and regulation.
  Curr Opin Chem Biol, 2, 633-641.  
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
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.  
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.  
  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.  
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.  
  8550407 Y.Li, and W.R.Strohl (1996).
Cloning, purification, and properties of a phosphotyrosine protein phosphatase from Streptomyces coelicolor A3(2).
  J Bacteriol, 178, 136-142.  
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.  
  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
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.  
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.  
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.