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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PSD93 PDZ1 DOMAIN
 
Authors :  M. Fiorentini, A. Kallehauge, O. Kristensen, J. S. Kastrup, M. Gajhede
Date :  22 Jun 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Delta2 Receptor Interacting Protein, Transferase, Dlg2, Maguk, Psd93, Pdz Domain, Chapsyn-110 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Fiorentini, A. K. Nielsen, O. Kristensen, J. S. Kastrup, M. Gajhede
Structure Of The First Pdz Domain Of Human Psd-93.
Acta Crystallogr. , Sect. F V. 65 1254 2009
PubMed-ID: 20054121  |  Reference-DOI: 10.1107/S1744309109043267

(-) Compounds

Molecule 1 - DISKS LARGE HOMOLOG 2
    ChainsA
    EC Number2.7.4.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPDZ1, RESIDUES 95-188
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPOSTSYNAPTIC DENSITY PROTEIN PSD-93, CHANNEL-ASSOCIATED PROTEIN OF SYNAPSE-110, CHAPSYN-110, PSD-93

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO49Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:133 , ARG A:147 , VAL A:148 , HOH A:2116BINDING SITE FOR RESIDUE SO4 A1191
2AC2SOFTWAREARG A:105 , GLY A:106 , ASN A:107 , SER A:108 , HOH A:2106 , HOH A:2120BINDING SITE FOR RESIDUE SO4 A1194
3AC3SOFTWAREGLU A:100 , THR A:102 , ARG A:145 , ARG A:154 , HOH A:2119BINDING SITE FOR RESIDUE SO4 A1192
4AC4SOFTWARETHR A:132 , ASN A:149 , ARG A:186BINDING SITE FOR RESIDUE CL A1193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WL7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WL7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WL7)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG2_MOUSE98-185
193-280
421-502
  1A:100-187
-
-
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG2_MOUSE98-185
193-280
421-502
  3A:100-187
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2WL7)

(-) Sequences/Alignments

Asymmetric 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:96
 aligned with DLG2_MOUSE | Q91XM9 from UniProtKB/Swiss-Prot  Length:852

    Alignment length:96
                                   102       112       122       132       142       152       162       172       182      
           DLG2_MOUSE    93 EYEFEEITLERGNSGLGFSIAGGTDNPHIGDDPGIFITKIIPGGAAAEDGRLRVNDCILRVNEVDVSEVSHSKAVEALKEAGSIVRLYVRRRRPIL 188
               SCOP domains d2wl7a_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --MAGPDZ-2wl7A01 A:100-184                                                                ------ Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeee............eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:100-187 UniProt: 98-185                                                     --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2wl7 A  95 EFEFEEITLERGNSGLGFSIAGGTDNPHIGDDPGIFITKIIPGGAAAEDGRLRVNDCILRVNEVDVSEVSHSKAVEALKEAGSIVRLYVRRRRPIL 190
                                   104       114       124       134       144       154       164       174       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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WL7)

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (DLG2_MOUSE | Q91XM9)
molecular function
    GO:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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: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:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    GO:0097120    receptor localization to synapse    Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0008328    ionotropic glutamate receptor complex    A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex.
    GO:0044224    juxtaparanode region of axon    A region of an axon near a node of Ranvier that is between the paranode and internode regions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008076    voltage-gated potassium channel complex    A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

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