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(-) Description

Title :  CRYSTAL STRUCTURE OF D1 AND D2 CATALYTIC DOMAINS OF HUMAN PROTEIN TYROSINE PHOSPHATASE GAMMA (D1+D2 PTPRG)
 
Authors :  P. Filippakopoulos, O. Gileadi, C. Johansson, E. Ugochukwu, A. Edward C. Arrowsmith, M. Sundstrom, F. Von Delft, S. Knapp, Structural Gen Consortium (Sgc)
Date :  20 Oct 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Ptprg, R-Ptp Gamma, Protein Tyrosine Phosphatase Gamma, D3S1249, Hptpg, Rptpg, Ptpg, D1-D2 Catalytic Domains, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Barr, E. Ugochukwu, W. H. Lee, O. N. 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 - PROTEIN TYROSINE PHOSPHATASE, RECEPTOR TYPE, G VARIANT (FRAGMENT)
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH
    Expression System Strain: ROSETTA-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTPRG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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 2NLK)

(-) Sites  (0, 0)

(no "Site" information available for 2NLK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:1319 -Pro A:1320

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NLK)

(-) PROSITE Motifs  (3, 5)

Asymmetric/Biological Unit (3, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTPRG_HUMAN848-1119
1150-1410		  2A:848-1119
A:1150-1410
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTPRG_HUMAN1036-1110
1327-1401		  2A:1036-1110
A:1327-1401
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTPRG_HUMAN1058-1068  1A:1058-1068

(-) Exons   (0, 0)

(no "Exon" information available for 2NLK)

(-) 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:553
 aligned with PTPRG_HUMAN | P23470 from UniProtKB/Swiss-Prot  Length:1445

    Alignment length:586
                                   836       846       856       866       876       886       896       906       916       926       936       946       956       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      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      
         PTPRG_HUMAN    827 AIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLPGKDSKHSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILGKETEVSSNQLHSYVNSILIPGVGGKTRLEKQFKLVTQCNAKYVECFSAQKECNKEKNRNSSVVPSERARVGLAPLPGMKGTDYINASYIMGYYRSNEFIITQHPLPHTTKDFWRMIWDHNAQIIVMLPDNQSLAEDEFVYWPSREESMNCEAFTVTLISKDRLCLSNEEQIIIHDFILEATQDDYVLEVRHFQCPKWPNPDAPISSTFELINVIKEEALTRDGPTIVHDEYGAVSAGMLCALTTLSQQLENENAVDVFQVAKMINLMRPGVFTDIEQYQFIYKAMLSLVS 1412
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nlkA01 A:827-1124 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                               ------------------     -------------       -----------------------------       -----------------------------------------------         --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh...........eee.....-----...eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhh..eeee....ee..ee..........eeee..eeeeeeeeee...eeeeeeeeee................eeeeeeeee...........hhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhh........hhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhh..-----hhhhhhhhhhh..-------.............................-------....eeee........eeeee..hhhhhhhhhhhhhhhh..eeee..---------..........eee..eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeee.........hhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------TYR_PHOSPHATASE_PTP  PDB: A:848-1119 UniProt: 848-1119                                                                                                                                                                                                                          ------------------------------TYR_PHOSPHATASE_PTP  PDB: A:1150-1410 UniProt: 1150-1410                                                                                                                                                                                                             -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1036-1110 UniProt: 1036-1110                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:1327-1401 UniProt: 1327-1401                     ----------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nlk A  827 AIPVKQFVKHIGELYSNNQHGFSEDFEEVQRCTADMNITAEHSNHPENKHKNRYINILAYDHSRVKLRPLP-----HSDYINANYVDGYNKAKAYIATQGPLKSTFEDFWRMIWEQNTGIIVMITNLVEKGRRKCDQYWPTENSEEYGNIIVTLKSTKIHACYTVRRFSIRNTKVKKGQKGNPKGRQNERVVIQYHYTQWPDMGVPEYALPVLTFVRRSSAARMPETGPVLVHCSAGVGRTGTYIVIDSMLQQIKDKSTVNVLGFLKHIRTQRNYLVQTEEQYIFIHDALLEAILGKETEVSSNQLHSYVNSILIP-----TRLEKQFKLVTQC-------FSAQKECNKEKNRNSSVVPSERARVGLAP-------DYINASYIMGYYRSNEFIITQHPLPHTTKDFWRMIWDHNAQIIVMLP---------FVYWPSREESMNCEAFTVTLISKDRLCLSNEEQIIIHDFILEATQDDYVLEVRHFQCPKWPNPDAPISSTFELINVIKEEALTRDGPTIVHDEYGAVSAGMLCALTTLSQQLENENAVDVFQVAKMINLMRPGVFTDIEQYQFIYKAMLSLVS 1412
                                   836       846       856       866       876       886       896|     |906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136     |   - |    1156   |     - |    1176      1186      1196      1206      1216      1226      1236      1246   |     -   |  1266      1276      1286      1296      1306      1316      1326      1336      1346      1356      1366      1376      1386      1396      1406      
                                                                                                897   903                                                                                                                                                                                                                                           1142  1148        1160    1168                        1196    1204                                          1250      1260
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2NLK)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTPRG_HUMAN | P23470)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0010633    negative regulation of epithelial cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:1903385    regulation of homophilic cell adhesion    Any process that modulates the frequency, rate or extent of homophilic cell adhesion.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTPRG_HUMAN | P23470: 2h4v 2hy3 2pbn 3jxh 3qcb 3qcc 3qcd 3qce 3qcf 3qcg 3qch 3qci 3qcj 3qck 3qcl 3qcm 3qcn 5e5r

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