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(-) Description

Title :  CIS FORM OF A PHOTOSWITCHABLE PDZ DOMAIN CROSSLINKED WITH AN AZOBENZENE DERIVATIVE
 
Authors :  R. Walser, O. Zerbe, P. Hamm
Date :  09 Nov 12  (Deposition) - 03 Jul 13  (Release) - 07 Aug 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Photoswitch, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Buchli, S. A. Waldauer, R. Walser, M. L. Donten, R. Pfister, N. Blochliger, S. Steiner, A. Caflisch, O. Zerbe, P. Hamm
Kinetic Response Of A Photoperturbed Allosteric Protein.
Proc. Natl. Acad. Sci. Usa V. 110 11725 2013
PubMed-ID: 23818626  |  Reference-DOI: 10.1073/PNAS.1306323110

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 13
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPET30A(+)
    FragmentPDZ 2 DOMAIN RESIDUES 1361-1456
    GenePTPN13, PNP1, PTP1E, PTPL1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFAS-ASSOCIATED PROTEIN-TYROSINE PHOSPHATASE 1, FAP-1, PTP- BAS, PROTEIN-TYROSINE PHOSPHATASE 1E, PTP-E1, HPTPE1, PROTEIN- TYROSINE PHOSPHATASE PTPL1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
133B1Ligand/Ion3,3'-(E)-DIAZENE-1,2-DIYLBIS{6-[(CHLOROACETYL)AMINO]BENZENESULFONIC ACID}
NMR Structure * (1, 1)
No.NameCountTypeFull Name
133B1Ligand/Ion3,3'-(E)-DIAZENE-1,2-DIYLBIS{6-[(CHLOROACETYL)AMINO]BENZENESULFONIC ACID}

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:22 , LYS A:39 , ALA A:40 , LYS A:73 , CYS A:77 , ARG A:80BINDING SITE FOR RESIDUE 33B A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M0Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M0Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016200L1419PPTN13_HUMANPolymorphism749353184AL60P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016200L1419PPTN13_HUMANPolymorphism749353184AL60P

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN13_HUMAN1093-1179
1368-1453
1501-1589
1788-1869
1883-1966
  1-
A:9-94
-
-
-
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN13_HUMAN1093-1179
1368-1453
1501-1589
1788-1869
1883-1966
  1-
A:9-94
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2M0Z)

(-) Sequences/Alignments

NMR Structure
   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:97
 aligned with PTN13_HUMAN | Q12923 from UniProtKB/Swiss-Prot  Length:2485

    Alignment length:97
                                  1369      1379      1389      1399      1409      1419      1429      1439      1449       
         PTN13_HUMAN   1360 PPKPGDIFEVELAKNDNSLGISVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVETLRNTGQVVHLLLEKGQSPT 1456
               SCOP domains d2m0za_ A: Phosphatase hPTP1e                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.......eeee...........eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------P------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: A:9-94 UniProt: 1368-1453                                                   --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                2m0z A    1 GPKPGDIFEVELAKNDNSLGICVTGGVNTSVRHGGIYVKAVIPQGAAESDGRIHKGDRVLAVNGVSLEGATHKQAVCTLRNTGQVVHLLLEKGQSPT   97
                                    10        20        30        40        50        60        70        80        90       

   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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M0Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M0Z)

(-) Gene Ontology  (19, 19)

NMR Structure(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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2m10 RELATED ID: 18833 RELATED DB: BMRB