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(-) Description

Title :  STRUCTURE OF THE PDZ DOMAIN OF TAX1 (HUMAN T-CELL LEUKEMIA VIRUS TYPE I) BINDING PROTEIN 3
 
Authors :  J. W. Murray, N. Shafqat, W. Yue, E. Pilka, C. Johannsson, E. Salah, C. Cooper, J. M. Elkins, A. C. Pike, A. Roos, P. Filippakopoulos, F. Von Delft, M. Wickstroem, C. Bountra, A. M. Edwards, C. H. Arrowsmith, U. Oppermann
Date :  30 Jul 08  (Deposition) - 12 Aug 08  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Wnt Signaling Pathway, Protein Binding, Nucleus, Cytoplasm, Pdz Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Murray, N. Shafqat, W. Yue, E. Pilka, C. Johannsson, E. Salah, C. Cooper, J. M. Elkins, A. C. Pike, A. Roos, P. Filippakopoulos, F. Von Delft, M. Wickstroem, C. Bountra, A. M. Edwards, C. H. Arrowsmith, U. Oppermann
The Structure Of The Pdz Domain Of Tax1Bp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TAX1-BINDING PROTEIN 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA-R3
    Expression System Taxid: 562
    Fragment: PDZ DOMAIN, RESIDUES 13-113
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TAX INTERACTION PROTEIN 1, TIP-1, GLUTAMINASE-INTERACTING PROTEIN, HUMAN T-CELL LEUKEMIA VIRUS TYPE I BINDING PROTEIN 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2IMD2Ligand/IonIMIDAZOLE
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:62 , GLU A:67 , MET A:87 , IMD A:1130 , ZN A:1131BINDING SITE FOR RESIDUE IMD A1129
2AC2SOFTWAREGLU A:62 , GLU A:67 , ILE A:68 , ASP A:84 , IMD A:1129 , ZN A:1131BINDING SITE FOR RESIDUE IMD A1130
3AC3SOFTWAREGLU A:62 , GLU A:67 , IMD A:1129 , IMD A:1130BINDING SITE FOR RESIDUE ZN A1131
4AC4SOFTWAREHIS A:19 , GLU A:48BINDING SITE FOR RESIDUE ZN A1132
5AC5SOFTWAREHIS A:90 , HOH A:2024 , HOH A:2081BINDING SITE FOR RESIDUE CL A1133

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VZ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VZ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073966I33TTX1B3_HUMANUnclassified  ---AI33T
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.TX1B3_HUMAN15-112  1A:15-112

(-) Exons   (0, 0)

(no "Exon" information available for 2VZ5)

(-) 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:111
 aligned with TX1B3_HUMAN | O14907 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:113
                                    20        30        40        50        60        70        80        90       100       110       120   
          TX1B3_HUMAN    11 AVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSML 123
               SCOP domains d2vz5a_ A: automated matches                                                                                      SCOP domains
               CATH domains 2vz5A00 A:11-128  [code=2.30.42.10, no name defined]                                                              CATH domains
               Pfam domains ------PDZ-2vz5A01 A:17-110                                                                          ------------- Pfam domains
         Sec.struct. author .eeeeeeee.eee..eee..eeeee....hhhhh..........eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeeee..--........ Sec.struct. author
                 SAPs(SNPs) ----------------------T------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:15-112 UniProt: 15-112                                                                ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2vz5 A  11 SMVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAGLQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQS--SMLSETEV 128
                                    20        30        40        50        60        70        80        90       100       110  |  | 125   
                                                                                                                                113  |       
                                                                                                                                   121
   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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TX1B3_HUMAN | O14907)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:0007266    Rho protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:2000009    negative regulation of protein localization to cell surface    Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to the cell surface.
    GO:0030111    regulation of Wnt signaling pathway    Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        TX1B3_HUMAN | O14907: 2kg2 2l4s 2l4t 3gj9 3sfj 4e3b 4nnl 4nnm

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