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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-027, A UBA DOMAIN FROM MOUSE CDNA
 
Authors :  H. Onuki, Y. Doi-Katayama, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 May 04  (Deposition) - 28 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Uba Domain, Mus Musculus, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Onuki, Y. Doi-Katayama, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of Rsgi Ruh-027, A Uba Domain From Mus Musculus Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBA/UBX 33.3 KDA PROTEIN
    ChainsA
    EngineeredYES
    Expression System PlasmidP030324-26
    Expression System Vector TypePLASMID
    FragmentUBA DOMAIN
    GeneBC006701
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS (E. COLI)
    SynonymRSGI RUH-027

 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 1WHC)

(-) Sites  (0, 0)

(no "Site" information available for 1WHC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.UBXN1_MOUSE1-42  1A:8-48

(-) Exons   (0, 0)

(no "Exon" information available for 1WHC)

(-) 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:64
 aligned with UBXN1_MOUSE | Q922Y1 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:82
                                  1                                                                           
                                  |  4        14        24        34        44        54        64        74  
           UBXN1_MOUSE    - ------MAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLETPLSHVLGREPTPSEQVGPEGSG 76
               SCOP domains d1whca_ A: UBA/UBX 33.3 kDa protein                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains --------UBA-1whcA01 A:9-45                   ------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhh..........-----------------..-... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------UBA  PDB: A:8-48 UniProt: 1-42            ---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  1whc A  1 GSSGSSGAELTALESLIEMGFPRGRAEKALALTGNQGIEAAMDWLMEHEDDPDVDEPLS-----------------GP-SSG 64
                                    10        20        30        40        50        |-         -      ||62  
                                                                                     59                60| |  
                                                                                                        61 |  
                                                                                                          62  

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  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  (0, 0)

(no "CATH Domain" information available for 1WHC)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: UBA (32)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (UBXN1_MOUSE | Q922Y1)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0036435    K48-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein.
    GO:0071796    K6-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 6 in the target protein.
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    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:1904293    negative regulation of ERAD pathway    Any process that stops, prevents or reduces the frequency, rate or extent of ERAD pathway.
    GO:0032435    negative regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:1903094    negative regulation of protein K48-linked deubiquitination    Any process that stops, prevents or reduces the frequency, rate or extent of protein K48-linked deubiquitination.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:2000157    negative regulation of ubiquitin-specific protease activity    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin-specific protease (deubiquitinase) activity.
cellular component
    GO:0034098    VCP-NPL4-UFD1 AAA ATPase complex    A multiprotein ATPase complex required for the efficient dislocation of ER-lumenal degradation substrates, and their subsequent proteolysis by the proteasome. In budding yeast, this complex includes Cdc48p, Npl4p and Ufd1p proteins. In mammals, this complex includes a hexamer of VCP/p97 (a cytosolic ATPase) and trimers of each of its cofactors UFD1L and NPL4 (NPLOC4) (e.g. a 6:3:3 stoichiometry).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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