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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
 
Authors :  J. E. Debreczeni, A. J. Barr, J. Eswaran, E. Ugochukwu, M. Sundstrom, J. C. Arrowsmith, A. Edwards, S. Knapp
Date :  23 Feb 06  (Deposition) - 09 Mar 06  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Hydrolase, Receptor Type Tyrosine Phosphatase J, Ptprj, Glycoprotein, Protein Phosphatase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. F. King, P. Filippakopoulos, I. Alfano, P. Savitsky, N. A. Burgess-Brown, S. Muller, S. Knapp
Large-Scale Structural Analysis Of The Classical Human Protein Tyrosine Phosphatome.
Cell(Cambridge, Mass. ) V. 136 352 2009
PubMed-ID: 19167335  |  Reference-DOI: 10.1016/J.CELL.2008.11.038

(-) Compounds

Molecule 1 - HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPNIC28-BSA4
    FragmentRESIDUES 1019-1311
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN-TYROSINE PHOSPHATASE ETA, R-PTP-ETA, HPTP ETA, PROTEIN-TYROSINE PHOSPHATASE RECEPTOR TYPE J, DENSITY-ENHANCED PHOSPHATASE 1, DEP-1, CD14 8 ANTIGEN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NI4Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:-16 , HIS A:-18BINDING SITE FOR RESIDUE NI A2302
2AC2SOFTWAREHIS A:-17 , HIS A:-19 , LYS A:1106 , HIS A:1277 , HOH A:2019 , CL A:2304BINDING SITE FOR RESIDUE NI A2303
3AC3SOFTWAREHIS A:-17 , HIS A:-19 , LYS A:1106 , NI A:2303BINDING SITE FOR RESIDUE CL A2304
4AC4SOFTWAREHOH A:2002 , HOH A:2005BINDING SITE FOR RESIDUE NI A2305
5AC5SOFTWAREHIS A:-19 , HOH A:2003 , HOH A:2004BINDING SITE FOR RESIDUE NI A2306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CFV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CFV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038417I1235TPTPRJ_HUMANPolymorphism11039554AI1235T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038417I1235TPTPRJ_HUMANPolymorphism11039554AI1235T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTPRJ_HUMAN1041-1298  1A:1041-1298
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRJ_HUMAN1216-1289  1A:1216-1289
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRJ_HUMAN1237-1247  1A:1237-1247
Biological Unit 1 (3, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTPRJ_HUMAN1041-1298  3A:1041-1298
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRJ_HUMAN1216-1289  3A:1216-1289
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRJ_HUMAN1237-1247  3A:1237-1247

(-) Exons   (0, 0)

(no "Exon" information available for 2CFV)

(-) Sequences/Alignments

Asymmetric 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:268
 aligned with PTPRJ_HUMAN | Q12913 from UniProtKB/Swiss-Prot  Length:1337

    Alignment length:344
                                   966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296    
         PTPRJ_HUMAN    957 FSRYSDAVSLPQDPGVICGAVFGCIFGALVIVTVGGFIFWRKKRKDAKNNEVSFSQIKPKKSKLIRVENFEAYFKKQQADSNCGFAEEYEDLKLVGISQPKYAAELAENRGKNRYNNVLPYDISRVKLSVQTHSTDDYINANYMPGYHSKKDFIATQGPLPNTLKDFWRMVWEKNVYAIIMLTKCVEQGRTKCEEYWPSKQAQDYGDITVAMTSEIVLPEWTIRDFTVKNIQTSESHPLRQFHFTSWPDHGVPDTTDLLINFRYLVRDYMKQSPPESPILVHCSAGVGRTGTFIAIDRLIYQIENENTVDVYGIVYDLRMHRPLMVQTEDQYVFLNQCVLDIVR 1300
               SCOP domains d2cfva_ A:                                    aut  omated      matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2cfvA00 A:-                                   19-  1300 Pr     otein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh-----------------------------------hhh--hhhh...-----.ee..hhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhh........hhhhhh..eeee........eeee...hhhhhhhhhhhhhhh...eeee..-----------.....--.eee..eeeeeeeeee.--.eeeeeeeee..--.eeeeeeee..---------.hhhhhhhhhhhh..--------.eeee....hhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------TYR_PHOSPHATASE_PTP  PDB: A:1041-1298 UniProt: 1041-1298                                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1216-1289 UniProt: 1216-1289                    ----------- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA----------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2cfv A  -19 HHHHSSGVDLG-----------------------------------TEN--LYFQSMK-----LIRVENFEAYFKKQQADSNCGFAEEYEDLKLVGISQPKYAAELAENRGKNRYNNVLPYDISRVKLSVQTHSTDDYINANYMPGYHSKKDFIATQGPLPNTLKDFWRMVWEKNVYAIIMLT-----------EYWPS--AQDYGDITVAMTSEIVL--WTIRDFTVKNIQ--ESHPLRQFHFT---------TTDLLINFRYLVRDY--------PILVHCSAGVGRTGTFIAIDRLIYQIENENTVDVYGIVYDLRMHRPLMVQTEDQYVFLNQCVLDIVR 1300
                                   -10|        -         -         -      | |- |    || -   |  1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136  |      -    |   |- |    1166       | -|     1186 |  | 1196    |    -    | 1216        |-      1236      1246      1256      1266      1276      1286      1296    
                                     -9                                  -8 | -5    0|  1020                                                                                                                   1139        1151   |  |            1174  |       1188  |      1201      1211          1225     1234                                                                  
                                                                           -6     1019                                                                                                                                         1155  |               1177          1191                                                                                                             
                                                                                                                                                                                                                                  1158                                                                                                                                              

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CFV)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A   (PTPRJ_HUMAN | Q12913)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0070097    delta-catenin binding    Interacting selectively and non-covalently with the delta subunit of the catenin complex.
    GO:0045295    gamma-catenin binding    Interacting selectively and non-covalently with the gamma subunit of the catenin complex.
    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:0051019    mitogen-activated protein kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase.
    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:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    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.
biological process
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0060242    contact inhibition    The cellular process in which cells stop growing or dividing in response to increased cell density.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    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:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:0010642    negative regulation of platelet-derived growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
    GO:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0043116    negative regulation of vascular permeability    Any process that reduces the extent to which blood vessels can be pervaded by fluid.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0051894    positive regulation of focal adhesion assembly    Any process that activates or increases the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PTPRJ_HUMAN | Q129132dle 2nz6

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