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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL LOBE OF THE HUMAN UBR5 HECT DOMAIN
 
Authors :  E. Matta-Camacho, G. Kozlov, M. Menade, K. Gehring
Date :  02 Dec 10  (Deposition) - 25 Jan 12  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ubr5, Edd, Hhyd, Mixed Alpha-Beta Fold, Ubiquitin Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Matta-Camacho, G. Kozlov, M. Menade, K. Gehring
Structure Of The Hect C-Lobe Of The Ubr5 E3 Ubiquitin Ligase.
Acta Crystallogr. , Sect. F V. 68 1158 2012
PubMed-ID: 23027739  |  Reference-DOI: 10.1107/S1744309112036937

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UBR5
    ChainsA, B
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL LOBE OF HECT DOMAIN
    GeneUBR5, EDD, EDD1, HYD, KIAA0896
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymE3 UBIQUITIN-PROTEIN LIGASE, HECT DOMAIN-CONTAINING 1, HYPERPLASTIC DISCS PROTEIN HOMOLOG, HHYD, PROGESTIN-INDUCED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3PT3)

(-) Sites  (0, 0)

(no "Site" information available for 3PT3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PT3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PT3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PT3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PT3)

(-) Exons   (0, 0)

(no "Exon" information available for 3PT3)

(-) Sequences/Alignments

Asymmetric 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:88
 aligned with UBR5_HUMAN | O95071 from UniProtKB/Swiss-Prot  Length:2799

    Alignment length:100
                                  2702      2712      2722      2732      2742      2752      2762      2772      2782      2792
          UBR5_HUMAN   2693 FTSFNDESGENAEKLLQFKRWFWSIVEKMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIK 2792
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------------.eeeee........eee....eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                3pt3 A 2693 FTSFNDESGENAEKLLQFKRWFWSIVEKMSMTERQDLVYFWTSSP------------PSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIK 2792
                                  2702      2712      2722      2732    |    -      2752      2762      2772      2782      2792
                                                                     2737         2750                                          

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with UBR5_HUMAN | O95071 from UniProtKB/Swiss-Prot  Length:2799

    Alignment length:107
                                  2695      2705      2715      2725      2735      2745      2755      2765      2775      2785       
          UBR5_HUMAN   2686 NVQMLISFTSFNDESGENAEKLLQFKRWFWSIVEKMSMTERQDLVYFWTSSPSLPASEEGFQPMPSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIK 2792
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhheeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------...eeeee........eeehhh.eeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                3pt3 B 2686 SVQMLISFTSFNDESGENAEKLLQFKRWFWSIVEKMSMTERQDLVYFWTSSP----------PMPSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIK 2792
                                  2695      2705      2715      2725      2735 |       -  |   2755      2765      2775      2785       
                                                                            2737       2748                                            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3PT3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PT3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PT3)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UBR5_HUMAN | O95071)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:2000780    negative regulation of double-strand break repair    Any process that stops, prevents or reduces the frequency, rate or extent of double-strand break repair.
    GO:1901315    negative regulation of histone H2A K63-linked ubiquitination    Any process that stops, prevents or reduces the frequency, rate or extent of histone H2A K63-linked ubiquitination.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0035413    positive regulation of catenin import into nucleus    Any process that increases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
    GO:0033160    positive regulation of protein import into nucleus, translocation    Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0050847    progesterone receptor signaling pathway    Any series of molecular signals generated as a consequence of a progesterone binding to its receptor.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    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: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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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        UBR5_HUMAN | O950711i2t 2qho

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