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(-) Description

Title :  T CELL PROTEIN-TYROSINE PHOSPHATASE STRUCTURE
 
Authors :  L. F. Iversen
Date :  21 Mar 02  (Deposition) - 08 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Tyrosine Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. F. Iversen, K. B. Moller, A. K. Pedersen, G. H. Peters, A. S. Petersen, H. S. Andersen, S. Branner, S. B. Mortensen, N. P. Moller
Structure Determination Of T Cell Protein-Tyrosine Phosphatase.
J. Biol. Chem. V. 277 19982 2002
PubMed-ID: 11907034  |  Reference-DOI: 10.1074/JBC.M200567200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T-CELL PROTEIN-TYROSINE PHOSPHATASE
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 2, TCPTP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1L8K)

(-) Sites  (0, 0)

(no "Site" information available for 1L8K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L8K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L8K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L8K)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN2_HUMAN5-275  1A:5-275
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN2_HUMAN190-266  1A:190-266
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN2_HUMAN214-224  1A:214-224

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003096601cENSE00001916061chr18:12884198-12884072127PTN2_HUMAN1-23231A:5-2319
1.2ENST000003096602ENSE00001211693chr18:12859253-1285916391PTN2_HUMAN24-54311A:24-5431
1.4ENST000003096604ENSE00001211690chr18:12836890-12836790101PTN2_HUMAN54-87341A:54-8734
1.5ENST000003096605ENSE00001183647chr18:12831040-1283094299PTN2_HUMAN88-120331A:88-12033
1.6ENST000003096606ENSE00001183642chr18:12825943-12825809135PTN2_HUMAN121-165451A:121-16545
1.7ENST000003096607ENSE00001183635chr18:12817364-12817155210PTN2_HUMAN166-235701A:166-23570
1.8ENST000003096608ENSE00001183630chr18:12814354-12814202153PTN2_HUMAN236-286511A:236-27742
1.9ENST000003096609ENSE00001183625chr18:12802150-12801969182PTN2_HUMAN287-347610--
1.10bENST0000030966010bENSE00001861628chr18:12794484-127933001185PTN2_HUMAN347-415690--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:273
 aligned with PTN2_HUMAN | P17706 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:273
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274   
           PTN2_HUMAN     5 IEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAK 277
               SCOP domains d1l8ka_ A: Tyrosine phosphatase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1l8kA00 A:5-277 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------Y_phosphatase-1l8kA01 A:42-274                                                                                                                                                                                                           --- Pfam domains
         Sec.struct. author .hhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhh...........eee.......eeeeeeeeehhhheeeeeee.....hhhhhhhhhhhh...eeee......................eee....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee...........hhhhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TYR_PHOSPHATASE_PTP  PDB: A:5-275 UniProt: 5-275                                                                                                                                                                                                                               -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:190-266 UniProt: 190-266                           ----------- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (3)
           Transcript 1 (1) Exon 1.1c          Exon 1.2  PDB: A:24-54         ---------------------------------Exon 1.5  PDB: A:88-120          Exon 1.6  PDB: A:121-165 UniProt: 121-165    Exon 1.7  PDB: A:166-235 UniProt: 166-235                             Exon 1.8  PDB: A:236-277 UniProt: 236-286  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.4  PDB: A:54-87            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1l8k A   5 IEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAK 277
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Phosphatase (121)

(-) Gene Ontology  (50, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN2_HUMAN | P17706)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0004726    non-membrane spanning protein tyrosine phosphatase activity    Catalysis of the reaction: non-membrane spanning protein tyrosine phosphate + H2O = non-membrane spanning protein tyrosine + phosphate.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0050860    negative regulation of T cell receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0050922    negative regulation of chemotaxis    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0060336    negative regulation of interferon-gamma-mediated signaling pathway    Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
    GO:1902206    negative regulation of interleukin-2-mediated signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-2-mediated signaling pathway.
    GO:1902215    negative regulation of interleukin-4-mediated signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-4-mediated signaling pathway.
    GO:0070104    negative regulation of interleukin-6-mediated signaling pathway    Any process that decreases the rate, frequency or extent of the series of molecular events generated as a consequence of interleukin-6 binding to a cell surface receptor.
    GO:0010888    negative regulation of lipid storage    Any process that decreases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:1902227    negative regulation of macrophage colony-stimulating factor signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of macrophage colony-stimulating factor signaling pathway.
    GO:0045650    negative regulation of macrophage differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation.
    GO:2000587    negative regulation of platelet-derived growth factor receptor-beta signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of platelet-derived growth factor receptor-beta signaling pathway.
    GO:1902233    negative regulation of positive thymic T cell selection    Any process that stops, prevents or reduces the frequency, rate or extent of positive thymic T cell selection.
    GO:1902212    negative regulation of prolactin signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of prolactin signaling pathway.
    GO:0061099    negative regulation of protein tyrosine kinase activity    Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity.
    GO:0010804    negative regulation of tumor necrosis factor-mediated signaling pathway    Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
    GO:0060339    negative regulation of type I interferon-mediated signaling pathway    Any process that decreases the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1903899    positive regulation of PERK-mediated unfolded protein response    Any process that activates or increases the frequency, rate or extent of the PERK-mediated unfolded protein response.
    GO:1902237    positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:1902202    regulation of hepatocyte growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of hepatocyte growth factor receptor signaling pathway.
    GO:0060334    regulation of interferon-gamma-mediated signaling pathway    Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005793    endoplasmic reticulum-Golgi intermediate compartment    A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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