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(-) Description

Title :  UFD1 EXHIBITS THE AAA-ATPASE FOLD WITH TWO DISTINCT UBIQUITIN INTERACTION SITES
 
Authors :  S. Park, R. Isaacson, H. T. Kim, P. A. Silver, G. Wagner
Date :  10 Apr 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (15x)
Keywords :  Ufd1, Double-Psi-Beta-Barrel, Protein Turnover (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Park, R. Isaacson, H. T. Kim, P. A. Silver, G. Wagner
Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct Ubiquitin Interaction Sites
Structure V. 13 995 2005
PubMed-ID: 16004872  |  Reference-DOI: 10.1016/J.STR.2005.04.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN FUSION DEGRADATION PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN DOMAIN, RESIDUES 1-208
    GeneUFD1, PIP3
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymUB FUSION PROTEIN 1, POLYMERASE-INTERACTING PROTEIN 3

 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 1ZC1)

(-) Sites  (0, 0)

(no "Site" information available for 1ZC1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZC1)

(-) Cis Peptide Bonds  (1, 15)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15Tyr A:65 -Pro A:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZC1)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR048W1YGR048W.1VII:589830-5909151086UFD1_YEAST1-3613611A:1-208208

(-) 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:208
 aligned with UFD1_YEAST | P53044 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           UFD1_YEAST     1 MFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYK 208
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------UFD1-1zc1A01 A:20-199                                                                                                                                                               --------- Pfam domains
         Sec.struct. author ..................eeeeeeeeeee..........hhhhh..eeee.hhhhhhhhh........eeee......eeeeeeeee.....eeee.hhhhhhh......eeeeeeee.....eeeee..hhhhh....hhhhhhhhhhh...ee...eeeeee..eeeeeeeeeee......ee.......eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-208 UniProt: 1-361 [INCOMPLETE]                                                                                                                                                               Transcript 1
                 1zc1 A   1 MFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYK 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        

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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  (0, 0)

(no "SCOP Domain" information available for 1ZC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZC1)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (UFD1_YEAST | P53044)
molecular function
    GO:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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: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.
biological process
    GO:0071712    ER-associated misfolded protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation.
    GO:0051974    negative regulation of telomerase activity    Any process that stops or reduces the activity of the enzyme telomerase, which catalyzes of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:0070651    nonfunctional rRNA decay    An rRNA catabolic process that results in the targeted detection and degradation of aberrant rRNAs contained within translationally defective ribosomes, thereby acting as a quality-control system.
    GO:1900182    positive regulation of protein localization to nucleus    Any process that activates or increases the frequency, rate or extent of protein localization to nucleus.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    GO:0030970    retrograde protein transport, ER to cytosol    The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon.
    GO:1990116    ribosome-associated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide encoded by an aberrant message and associated with a stalled ribosome. Degradation is initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the ribosome-associated protein.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0071629    ubiquitin-dependent catabolism of misfolded proteins by cytoplasm-associated proteasome    The chemical reactions and pathways resulting in the breakdown of misfolded proteins in the cytoplasm, which are targeted to cytoplasmic proteasomes for degradation.
    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:0000837    Doa10p ubiquitin ligase complex    A multiprotein complex that recognizes and ubiquitinates membrane proteins with misfolded cytosolic domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Ssm4p/Doa10p.
    GO:0000839    Hrd1p ubiquitin ligase ERAD-L complex    A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p.
    GO:1990112    RQC complex    A multiprotein complex that forms a stable complex with 60S ribosomal subunits containing stalled polypeptides and triggers their degradation (ribosomal quality control). In budding yeast, this complex includes Cdc48p, Rkr1p, Tae2p, Rqc1p, Npl4p and Ufd1p proteins.
    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: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.

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    Tyr A:65 - Pro A:66   [ RasMol ]  
 

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