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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE SECOND PDZ DOMAIN OF HUMAN DLG3
 
Authors :  E. Ugochukwu, C. Phillips, G. Schoch, G. Berridge, E. Salah, S. Colebro C. Smee, P. Savitsky, J. Bray, J. Elkins, D. Doyle, G. Bunkoczi, J. Debr A. Turnbull, F. Gorrec, F. Von Delft, M. Sundstrom, C. Arrowsmith, J. A. Edwards, Structural Genomics Consortium (Sgc)
Date :  15 Dec 05  (Deposition) - 27 Dec 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdz Domain, Dlg3, Human, Structural Genomics, Structural Genomics Consortium, Sgc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ugochukwu, C. Phillips, G. Schoch, G. Berridge, E. Salah, S. Colebrook, C. Smee, P. Savitsky, J. Bray, J. Elkins, D. Doyle, G. Bunkoczi, J. Debreczeni, A. Turnbull, F. Gorrec, F. Von Delft, M. Sundstrom, C. Arrowsmith, J. Weigelt, A. Edwards, Structural Genomics Consortium (Sgc)
The Crystal Structure Of The Second Pdz Domain Of Human Dlg
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PRESYNAPTIC PROTEIN SAP102
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid562
    FragmentPDZ2
    GeneDLG3, KIAA1232
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSYNAPSE-ASSOCIATED PROTEIN 102, NEUROENDOCRINE-DLG, NE-DLG, DISCS LARGE HOMOLOG 3, DLG3, DLG3A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:107 , HOH A:126 , HOH A:175 , ASN A:228 , GLN A:247 , ASN A:253 , ARG A:271BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREHOH A:119 , HOH A:131 , HOH A:132 , HOH A:177 , LYS A:231 , LYS A:234 , GLY A:235 , LEU A:236 , GLY A:237 , LYS A:299BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FE5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FE5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FE5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DLG3_HUMAN131-218
226-313
386-467
  1-
A:226-313
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003743601bENSE00001958108X:69664819-69665408590DLG3_HUMAN1-1191190--
1.3ENST000003743603ENSE00000672255X:69668763-6966881351DLG3_HUMAN120-136170--
1.4ENST000003743604ENSE00000672253X:69669209-69669333125DLG3_HUMAN137-178420--
1.5ENST000003743605ENSE00000672252X:69669540-69669709170DLG3_HUMAN178-235581A:221-23515
1.6aENST000003743606aENSE00000436378X:69670019-69670155137DLG3_HUMAN235-280461A:235-28046
1.6cENST000003743606cENSE00000672250X:69670489-69670633145DLG3_HUMAN281-329491A:281-31434
1.7ENST000003743607ENSE00000672249X:69671717-69671876160DLG3_HUMAN329-382540--
1.9ENST000003743609ENSE00001599030X:69673487-69673643157DLG3_HUMAN382-434530--
1.10ENST0000037436010ENSE00000672247X:69674064-69674166103DLG3_HUMAN435-469350--
1.13bENST0000037436013bENSE00001675478X:69699000-69699114115DLG3_HUMAN469-507390--
1.14bENST0000037436014bENSE00000672235X:69711957-69712133177DLG3_HUMAN507-566600--
1.15ENST0000037436015ENSE00000436409X:69712371-6971244676DLG3_HUMAN566-591260--
1.17ENST0000037436017ENSE00000815626X:69715258-6971530346DLG3_HUMAN592-607160--
1.19bENST0000037436019bENSE00000672149X:69718370-6971842051DLG3_HUMAN607-624180--
1.20ENST0000037436020ENSE00001705646X:69719026-69719127102DLG3_HUMAN624-658350--
1.21bENST0000037436021bENSE00000672147X:69719727-69719899173DLG3_HUMAN658-715580--
1.22aENST0000037436022aENSE00000672146X:69720321-69720430110DLG3_HUMAN716-752370--
1.22cENST0000037436022cENSE00000436391X:69720748-6972083992DLG3_HUMAN752-783320--
1.23cENST0000037436023cENSE00001154826X:69722013-697253373325DLG3_HUMAN783-817350--

(-) 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:94
 aligned with DLG3_HUMAN | Q92796 from UniProtKB/Swiss-Prot  Length:817

    Alignment length:94
                                   230       240       250       260       270       280       290       300       310    
           DLG3_HUMAN   221 PETIMEVNLLKGPKGLGFSIAGGIGNQHIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPGS 314
               SCOP domains --d2fe5a1 A:223-314 Synapse-associated protein 102                                             SCOP domains
               CATH domains 2fe5A00 A:221-314  [code=2.30.42.10, no name defined]                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeeee............eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:226-313 UniProt: 226-313                                                    - PROSITE
           Transcript 1 (1) Exon 1.5       ---------------------------------------------Exon 1.6c  PDB: A:281-314          Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.6a  PDB: A:235-280 UniProt: 235-280    ---------------------------------- Transcript 1 (2)
                 2fe5 A 221 SMTIMEVNLLKGPKGLGFSIAGGIGNQHIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPGS 314
                                   230       240       250       260       270       280       290       300       310    

   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: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FE5)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DLG3_HUMAN | Q92796)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    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:0015276    ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
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:0001736    establishment of planar polarity    Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates.
    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:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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.
cellular component
    GO:0032281    AMPA glutamate receptor complex    An 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. The AMPA receptors mediate fast synaptic transmission in the CNS and are composed of subunits GluR1-4, products from separate genes. These subunits have an extracellular N-terminus and an intracellular C-terminus.
    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: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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043198    dendritic shaft    Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DLG3_HUMAN | Q927961um7 2i1n

(-) Related Entries Specified in the PDB File

2byg 2ND PDZ DOMAIN OF DISCS LARGE HOMOLOGUE 2