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(-) Description

Title :  UNVEILING THE STRUCTURAL DETERMINANTS OF KIAA0323 BINDING PREFERENCE FOR NEDD8
 
Authors :  E. Santonico, R. Nepravishta, A. Mattioni, E. Valentini, W. Mandaliti R. Procopio, M. Iannuccelli, L. Castagnoli, S. Polo, M. Paci, G. Cesar
Date :  14 Sep 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (11x)
NMR Structure *:  A,B  (1x)
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Santonico, R. Nepravishta, A. Mattioni, E. Valentini, W. Mandaliti, R. Procopio, M. Iannuccelli, L. Castagnoli, S. Polo, M. Paci, G. Cesareni
Unveiling The Structural Determinants Of Kiaa0323 Binding Preference For Nedd8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NEDD8
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX6P1
    GeneNEDD8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8
 
Molecule 2 - PROTEIN KHNYN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPGEX6P1
    FragmentRESIDUES 627-678
    GeneKHNYN, KIAA0323
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKH AND NYN DOMAIN-CONTAINING PROTEIN

 Structural Features

(-) Chains, Units

  12
NMR Structure (11x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2N7K)

(-) Sites  (0, 0)

(no "Site" information available for 2N7K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2N7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2N7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2N7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2N7K)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002504951aENSE00001101093chr14:24701660-24701456205NEDD8_HUMAN1-661A:1-66
1.4ENST000002504954ENSE00002175755chr14:24687637-2468759048NEDD8_HUMAN7-22161A:7-2216
1.5aENST000002504955aENSE00002178617chr14:24687421-2468733983NEDD8_HUMAN23-50281A:23-5028
1.6eENST000002504956eENSE00001549615chr14:24686429-24686058372NEDD8_HUMAN50-81321A:50-7627

(-) 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:76
 aligned with NEDD8_HUMAN | Q15843 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:76
                                    10        20        30        40        50        60        70      
          NEDD8_HUMAN     1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhh.eee..ee.....hhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a  Exon 1.4        Exon 1.5a  PDB: A:23-50     -------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6e  PDB: A:50-76     Transcript 1 (2)
                 2n7k A   1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG  76
                                    10        20        30        40        50        60        70      

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with KHNYN_HUMAN | O15037 from UniProtKB/Swiss-Prot  Length:678

    Alignment length:52
                                   636       646       656       666       676  
          KHNYN_HUMAN   627 GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF 678
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh.........hhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 2n7k B  77 GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF 128
                                    86        96       106       116       126  

   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  (0, 0)

(no "SCOP Domain" information available for 2N7K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2N7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2N7K)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (NEDD8_HUMAN | Q15843)
molecular function
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0045116    protein neddylation    Covalent attachment of the ubiquitin-like protein NEDD8 (RUB1) to another protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    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: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.

Chain B   (KHNYN_HUMAN | O15037)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KHNYN_HUMAN | O150372n5m
        NEDD8_HUMAN | Q158431ndd 1r4m 1r4n 1xt9 2bkr 2ko3 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4f8c 4fbj 4hcp 4p5o

(-) Related Entries Specified in the PDB File

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