Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PTPL1 HUMAN TYROSINE PHOSPHATASE MUTATED IN COLORECTAL CANCER - EVIDENCE FOR A SECOND PHOSPHOTYROSINE SUBSTRATE RECOGNITION POCKET
 
Authors :  F. Villa, M. Deak, G. B. Bloomberg, D. R. Alessi, D. M. F. Van Aalten
Date :  16 Nov 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Tyrosine Phosphatase, Phosphate Ion, Colorectal Cancer Alternative Splicing, Coiled Coil, Cytoskeleton, Polymorphism, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Villa, M. Deak, G. B. Bloomberg, D. R. Alessi, D. M. F. Van Aalten
Crystal Structure Of Ptpl1/Fap-1 Human Tyrosine Phosphatase Mutated In Colorectal Cancer: Eveidence For A Second Phosphotyrosine Substrate Recognition Pocket
J. Biol. Chem. V. 280 8180 2005
PubMed-ID: 15611135  |  Reference-DOI: 10.1074/JBC.M412211200

(-) Compounds

Molecule 1 - PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 13
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6_1
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentRESIDUES 2163-2477
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN TYROSINE PHOSPHATASE LIKE 1, PROTEIN TYROSINE PHOSPHATASE 1E, PTP-E1, HPTPE1, PTP-BAS, PROTEIN TYROSINE PHOSPHATASE PTPL1, FAS-ASSOCIATED PROTEIN TYROSINE PHOSPHATASE 1, FAP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:2378 , CYS A:2408 , SER A:2409 , ALA A:2410 , GLY A:2411 , ILE A:2412 , GLY A:2413 , ARG A:2414 , GLN A:2452 , HOH A:3260 , HOH A:3275BINDING SITE FOR RESIDUE PO4 A3478
2AC2SOFTWARESER A:2334 , ASN A:2335 , ARG A:2336 , HOH A:3277BINDING SITE FOR RESIDUE PO4 A3479
3AC3SOFTWAREGLN A:2310 , GLU A:2311 , ASN A:2372 , THR A:2374 , HOH A:3278 , HOH A:3279 , HOH A:3280BINDING SITE FOR RESIDUE PO4 A3480

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048361I2458VPTN13_HUMANPolymorphism34226837AI2458V

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_PTPPS50055 PTP type protein phosphatase family profile.PTN13_HUMAN2213-2467  1A:2213-2467
2TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.PTN13_HUMAN2389-2458  1A:2389-2458

(-) Exons   (0, 0)

(no "Exon" information available for 1WCH)

(-) 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:308
 aligned with PTN13_HUMAN | Q12923 from UniProtKB/Swiss-Prot  Length:2485

    Alignment length:308
                                  2179      2189      2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299      2309      2319      2329      2339      2349      2359      2369      2379      2389      2399      2409      2419      2429      2439      2449      2459      2469        
         PTN13_HUMAN   2170 HSFLTNDELAVLPVVKVLPSGKYTGANLKSVIRVLRGLLDQGIPSKELENLQELKPLDQCLIGQTKENRRKNRYKNILPYDATRVPLGDEGGYINASFIKIPVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWPNILGKTTMVSNRLRLALVRMQQLKGFVVRAMTLEDIQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIHRSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTRLQAEEEQ 2477
               SCOP domains d1wcha_ A: Tyrosine-protein phosphatase, non-receptor type 13 (PTPL1)                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1wchA00 A:2170-2477 Protein tyrosine phosphatase superfamily                                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------Y_phosphatase-1wchA01 A:2237-2466                                                                                                                                                                                                     ----------- Pfam domains
         Sec.struct. author ....hhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.........................eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhh...eeee....ee..ee.............ee....eeeeeeeeee...eeeeeeeeee....eeeeeeeeee..........hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------TYR_PHOSPHATASE_PTP  PDB: A:2213-2467 UniProt: 2213-2467                                                                                                                                                                                                       ---------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:2389-2458 UniProt: 2389-2458                ------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wch A 2170 HSFLTNDELAVLPVVKVLPSGKYTGANLKSVIRVLRGLLDQGIPSKELENLQELKPLDQCLIGQTKENRRKNRYKNILPYDATRVPLGDEGGYINASFIKIPVGKEEFVYIACQGPLPTTVGDFWQMIWEQKSTVIAMMTQEVEGEKIKCQRYWPNILGKTTMVSNRLRLALVRMQQLKGFVVRAMTLEDIQTREVRHISHLNFTAWPDHDTPSQPDDLLTFISYMRHIHRSGPIITHCSAGIGRSGTLICIDVVLGLISQDLDFDISDLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTRLQAEEEQ 2477
                                  2179      2189      2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299      2309      2319      2329      2339      2349      2359      2369      2379      2389      2399      2409      2419      2429      2439      2449      2459      2469        

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTN13_HUMAN | Q12923)
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:0036312    phosphatidylinositol 3-kinase regulatory subunit binding    Interacting selectively and non-covalently with a regulatory subunit of phosphatidylinositol 3-kinase. The regulatory subunit associates with the catalytic subunit to regulate both its activity and subcellular location.
    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.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
cellular component
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wch)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wch
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PTN13_HUMAN | Q12923
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.48
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PTN13_HUMAN | Q12923
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PTN13_HUMAN | Q129231d5g 1q7x 2m0z 2m10 3lnx 3lny 3pdz 5glj

(-) Related Entries Specified in the PDB File

1d5g SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMANPHOSPHATASE HPTP1E COMPLEXED WITH A PEPTIDE
1q7x SOLUTION STRUCTURE OF THE ALTERNATIVELY SPLICED PDZ2 DOMAIN(PDZ2B) OF PTP-BAS (HPTP1E)
3pdz SOLUTION STRUCTURE OF THE PDZ2 DOMAIN FROM HUMAN PHOSPHATASE HPTP1E