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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HEPTP CATALYTIC DOMAIN D236A MUTANT
 
Authors :  D. A. Critton, A. Tortajada, R. Page
Date :  20 Jun 07  (Deposition) - 24 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Heptp, Human Hematopoietic Tyrosine Phosphatase Catalytic Domain Mutant, Lc-Ptp, Ptpn7, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Critton, A. Tortajada, G. Stetson, W. Peti, R. Page
Structural Basis Of Substrate Recognition By Hematopoietic Tyrosine Phosphatase.
Biochemistry V. 47 13336 2008
PubMed-ID: 19053285  |  Reference-DOI: 10.1021/BI801724N

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 7
    Chains: A
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (RESIDUES 65-360)
    Gene: PTPN7
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE LC-PTP, HEMATOPOIETIC PROTEIN- TYROSINE PHOSPHATASE, HEPTP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:270 , SER A:271 , ALA A:272 , GLY A:273 , ILE A:274 , GLY A:275 , ARG A:276 , GLN A:314 , HOH A:503 , HOH A:701BINDING SITE FOR RESIDUE PO4 A 436
2AC2SOFTWARETHR A:174 , GLN A:175 , SER A:271 , ARG A:276 , HOH A:527 , HOH A:533 , HOH A:645BINDING SITE FOR RESIDUE PO4 A 437
3AC3SOFTWAREGLN A:112 , GLU A:222 , ARG A:223 , ARG A:224 , HOH A:632 , HOH A:716 , HOH A:728 , HOH A:729BINDING SITE FOR RESIDUE GOL A 501
4AC4SOFTWAREGLN A:112 , SER A:113 , TYR A:133 , GLU A:141 , HOH A:526 , HOH A:531 , HOH A:571 , HOH A:647 , HOH A:716 , HOH A:728BINDING SITE FOR RESIDUE GOL A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN7_HUMAN97-350  1A:76-329
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN7_HUMAN268-341  1A:247-320
3TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.PTN7_HUMAN289-299  1A:268-278

(-) Exons   (0, 0)

(no "Exon" information available for 2QDC)

(-) 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:284
 aligned with PTN7_HUMAN | P35236 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:291
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355 
           PTN7_HUMAN    66 TPREVTLHFLRTAGHPLTRWALQRQPPSPKQLEEEFLKIPSNFVSPEDLDIPGHASKDRYKTILPNPQSRVCLGRAQSQEDGDYINANYIRGYDGKEKVYIATQGPMPNTVSDFWEMVWQEEVSLIVMLTQLREGKEKCVHYWPTEEETYGPFQIRIQDMKECPEYTVRQLTIQYQEERRSVKHILFSAWPDHQTPESAGPLLRLVAEVEESPETAAHPGPIVVHCSAGIGRTGCFIATRIGCQQLKARGEVDILGIVCQLRLDRGGMIQTAEQYQFLHHTLALYAGQLPE 356
               SCOP domains d2qdca_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2qdcA00 A:45-335 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                           CATH domains
               Pfam domains -----------------------------------------------------Y_phosphatase-2qdcA01 A:98-328                                                                                                                                                                                                         ------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..eeehhhhhhh..hhhhhhhhhhhh.....hhhhh...hhhhhh.......hhh.eee...........eeeeeee.hhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeee...-------.......eeee..eeeeeeeeee...eeeeeeeeee..eeeeeeeeee..........hhhhhhhhhhhhhh..........eeeee...hhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------TYR_PHOSPHATASE_PTP  PDB: A:76-329 UniProt: 97-350                                                                                                                                                                                                            ------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:247-320 UniProt: 268-341                        --------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA--------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qdc A  45 TPREVTLHFLRTAGHPLTRWALQRQPPSPKQLEEEFLKIPSNFVSPEDLDIPGHASKDRYKTILPNPQSRVCLGRAQSQEDGDYINANYIRGYDGKEKVYIATQGPMPNTVSDFWEMVWQEEVSLIVMLTQL-------VHYWPTEEETYGPFQIRIQDMKECPEYTVRQLTIQYQEERRSVKHILFSAWPAHQTPESAGPLLRLVAEVEESPETAAHPGPIVVHCSAGIGRTGCFIATRIGCQQLKARGEVDILGIVCQLRLDRGGMIQTAEQYQFLHHTLALYAGQLPE 335
                                    54        64        74        84        94       104       114       124       134       144       154       164       174 |     184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
                                                                                                                                                             176     184
   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  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN7_HUMAN | P35236)
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: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.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN7_HUMAN | P35236: 1zc0 2a3k 2gp0 2gph 2hvl 2qdm 2qdp 3d42 3d44 3o4s 3o4t 3o4u

(-) Related Entries Specified in the PDB File

1zc0 2gp0 2hvl