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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN OF PALS1 PROTEIN
 
Authors :  X. -R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Feb 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Palmitoylated 5, Pals1 Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. -R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Pdz Domain Of Pals1 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAGUK P55 SUBFAMILY MEMBER 5
    ChainsA
    EngineeredYES
    Expression System PlasmidP030203-38
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneRIKEN CDNA 3830420B02
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymPALS1 PROTEIN, PROTEIN ASSOCIATED WITH LIN-7 1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VA8)

(-) Sites  (0, 0)

(no "Site" information available for 1VA8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VA8)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.MPP5_MOUSE256-336  1A:28-107
2SH3PS50002 Src homology 3 (SH3) domain profile.MPP5_MOUSE345-417  1A:110-111

(-) Exons   (0, 0)

(no "Exon" information available for 1VA8)

(-) 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:113
 aligned with MPP5_MOUSE | Q9JLB2 from UniProtKB/Swiss-Prot  Length:675

    Alignment length:189
                                   182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352         
           MPP5_MOUSE   173 MSKASPPFPLIANVQDLVQEVQTVLKPVHQKEGQELTALLNAPHIQALLLAHDKVAEQEMQLEPITDERVYESIGHYGGETVKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLSDMHGTLTFVLIPSQQIKPPPAKETVIHVKAHFDYDPSDD 361
               SCOP domains ---------------------------------------------------------------d1va8a1 A:8-107 Maguk p55 subfamily member 5                                                        -------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------1va8A01 A:19-106  [code=2.30.42.10, no name defined]                                    --------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------PDZ-1va8A01 A:29-105                                                         ---------------------------- Pfam domains
         Sec.struct. author .......--------------------------------------------------------............ee..ee.eeeeeee.......eeeee....eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh.eeeeeeee...--------------------..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------PDZ  PDB: A:28-107 UniProt: 256-336                                              --------SH3               PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1va8 A   1 GSSGSSG--------------------------------------------------------PITDERVYESIGHYGGETVKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKSGLLHEGDEVLEINGIEIRGKDVNEVFDLLSDMHGTLTFVLIPSS--------------------GPSSG 113
                                  |  -         -         -         -         -         -   |    14        24        34        44        54        64        74        84        94       104   |     -         -    |    
                                  7                                                        8                                                                                                 108                  109    

   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  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (MPP5_MOUSE | Q9JLB2)
molecular function
    GO:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0046710    GDP metabolic process    The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
    GO:0046037    GMP metabolic process    The chemical reactions and pathways involving GMP, guanosine monophosphate.
    GO:0070830    bicellular tight junction assembly    The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
    GO:0090162    establishment of epithelial cell polarity    The specification and formation of anisotropic intracellular organization of an epithelial cell.
    GO:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    GO:0002011    morphogenesis of an epithelial sheet    The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells.
    GO:0032288    myelin assembly    The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system.
    GO:0032287    peripheral nervous system myelin maintenance    The process in which the structure and material content of mature peripheral nervous system myelin is kept in a functional state.
    GO:0007009    plasma membrane organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
    GO:0035750    protein localization to myelin sheath abaxonal region    Any process in which a protein is transported to, and/or maintained in, the abaxonal region of the myelin sheath. The abaxonal region is the region of the myelin sheath furthest from the axon.
cellular component
    GO:0043220    Schmidt-Lanterman incisure    Regions within compact myelin in which the cytoplasmic faces of the enveloping myelin sheath are not tightly juxtaposed, and include cytoplasm from the cell responsible for making the myelin. Schmidt-Lanterman incisures occur in the compact myelin internode, while lateral loops are analogous structures found in the paranodal region adjacent to the nodes of Ranvier.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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:0043219    lateral loop    Non-compact myelin located adjacent to the nodes of Ranvier in a myelin segment. These non-compact regions include cytoplasm from the cell responsible for synthesizing the myelin. Lateral loops are found in the paranodal region adjacent to the nodes of Ranvier, while Schmidt-Lantermann clefts are analogous structures found within the compact myelin internode.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0035749    myelin sheath adaxonal region    The region of the myelin sheath nearest to the axon.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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        MPP5_MOUSE | Q9JLB21vf6

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