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(-) Description

Title :  SOLUTION STRUCTURE OF THE RNEDD4 WWIII DOMAIN-RENAC BP2 PEPTIDE COMPLEX
 
Authors :  V. Kanelis, D. Rotin, J. D. Forman-Kay
Date :  27 Feb 01  (Deposition) - 02 May 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  B,W  (15x)
Keywords :  Nedd4, Ww Domains, Enac, Py Motif, Liddle Syndrome, Nmr, Proline-Rich, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Kanelis, D. Rotin, J. D. Forman-Kay
Solution Structure Of A Nedd4 Ww Domain-Enac Peptide Complex.
Nat. Struct. Biol. V. 8 407 2001
PubMed-ID: 11323714  |  Reference-DOI: 10.1038/87562
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN LIGASE NEDD4
    Chains: W
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: WWIII DOMAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: RNEDD4
 
Molecule 2 - AMILORIDE-SENSITIVE SODIUM CHANNEL BETA-SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: AN IDENTICAL PEPTIDE WAS MADE SYNTHETICALLY USING STANDARD F-MOC CHEMISTRY FOR NMR SAMPLES REQUIRING UNLABELED BP2 PEPTIDE.
    Synonym: RENAC BP2 PEPTIDE

 Structural Features

(-) Chains, Units

  
NMR Structure (15x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1I5H)

(-) Sites  (0, 0)

(no "Site" information available for 1I5H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I5H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I5H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I5H)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.NEDD4_RAT246-279
402-435
459-492		  1-
-
W:459-492
2WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.NEDD4_RAT252-277
408-433
465-490		  1-
-
W:465-490

(-) Exons   (0, 0)

(no "Exon" information available for 1I5H)

(-) 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 B from PDB  Type:PROTEIN  Length:17
 aligned with SCNNB_RAT | P37090 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:51
                                   580       590       600       610       620 
            SCNNB_RAT   571 GPPPTVAELVEAHTNFGFQPDTTSCRPNAEVYPDQQTLPIPGTPPPNYDSL 621
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .----------------------------------................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 1i5h B 605 G----------------------------------STLPIPGTPPPNYDSL 621
                            |        -         -         -     | 610       620 
                          605                                606               


Chain W from PDB  Type:PROTEIN  Length:50
 aligned with NEDD4_RAT | Q62940 from UniProtKB/Swiss-Prot  Length:887

    Alignment length:51
                                   458       468       478       488       498 
            NEDD4_RAT   449 GKTPVDSNDLGPLPPGWEERTHTDGRVFFINHNIKKTQWEDPRMQNVAITG 499
               SCOP domains d 1i5hw_ W: Ubiquitin ligase NEDD4 WWIII domain     SCOP domains
               CATH domains 1 i5hW00 W:450-499                                  CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .-..............eeeee.....eeeee....eee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------WW_DOMAIN_2  PDB: W:459-492       ------- PROSITE (1)
                PROSITE (2) ----------------WW_DOMAIN_1  PDB: W:465-49--------- PROSITE (2)
                 Transcript --------------------------------------------------- Transcript
                 1i5h W 450 G-SPVDSNDLGPLPPGWEERTHTDGRVFFINHNIKKTQWEDPRMQNVAITG 499
                            | |    458       468       478       488       498 
                            | |                                                
                          450 |                                                
                            451
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I5H)

(-) Gene Ontology  (39, 42)

NMR Structure(hide GO term definitions)
Chain B   (SCNNB_RAT | P37090)
molecular function
    GO:0050699    WW domain binding    Interacting selectively and non-covalently with a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions.
    GO:0015280    ligand-gated sodium channel activity    Enables the transmembrane transfer of a sodium ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
    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:0005272    sodium channel activity    Enables the facilitated diffusion of a sodium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0050891    multicellular organismal water homeostasis    Any process involved in the maintenance of an internal steady state of water within a tissue, organ, or a multicellular organism.
    GO:0002028    regulation of sodium ion transport    Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0050909    sensory perception of taste    The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process.
    GO:0055078    sodium ion homeostasis    Any process involved in the maintenance of an internal steady state of sodium ions within an organism or cell.
    GO:0035725    sodium ion transmembrane transport    A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006814    sodium ion transport    The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0035313    wound healing, spreading of epidermal cells    The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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:0034706    sodium channel complex    An ion channel complex through which sodium ions pass.

Chain W   (NEDD4_RAT | Q62940)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0030948    negative regulation of vascular endothelial growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    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:0070534    protein K63-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is added to a protein. K63-linked ubiquitination does not target the substrate protein for degradation, but is involved in several pathways, notably as a signal to promote error-free DNA postreplication repair.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0048814    regulation of dendrite morphogenesis    Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
    GO:0014894    response to denervation involved in regulation of muscle adaptation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a denervation stimulus. This process occurs as part of the regulation of muscle adaptation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    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
        NEDD4_RAT | Q62940: 2n8s 2n8t 2n8u

(-) Related Entries Specified in the PDB File

4963 4963 IS CHEMICAL SHIFTS FOR THE WW DOMAIN AND THE BP2 PEPTIDE. COUPLING CONSTANTS FOR THE WW DOMAIN (J-HNHA AND LONG RANGE J-CC) AND THE BP2 PEPTIDE (J-HNHA AND J-HAHB) ARE PROVIDED AS WELL.