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(-) Description

Authors :  J. R. Walker, G. V. Avvakumov, S. Xue, E. M. Newman, F. Mackenzie, J. Weig M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, S. Dhe-Pagano Structural Genomics Consortium (Sgc)
Date :  28 Jun 05  (Deposition) - 12 Jul 05  (Release) - 28 Nov 12  (Revision)
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Alternative Splicing; Nuclear Protein; Ubl Conjugation Pathway, Ubiquitin, Ubiquitin- Conjugating Enzyme, Ligase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. Sheng, J. H. Hong, R. Doherty, T. Srikumar, J. Shloush, G. V. Avvakumov, J. R. Walker, S. Xue, D. Neculai, J. W. Wan, S. K. Kim, C. H. Arrowsmith, B. Raught, S. Dhe-Paganon
A Human Ubiquitin Conjugating Enzyme (E2)-Hect E3 Ligase Structure-Function Screen.
Mol Cell Proteomics V. 11 329 2012
PubMed-ID: 22496338  |  Reference-DOI: 10.1074/MCP.O111.013706

(-) Compounds

    EC Number6.3.2.19
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneUBE2V1, CROC1, UBE2V, UEV1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2A4D)

(-) Sites  (0, 0)

(no "Site" information available for 2A4D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A4D)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Tyr A:149 -Pro A:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A4D)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1UBIQUITIN_CONJUGAT_2PS50127 Ubiquitin-conjugating enzymes family profile.UB2V1_HUMAN15-140  1A:89-214

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

Asymmetric/Biological 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:139
 aligned with UB2V1_HUMAN | Q13404 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137         
               SCOP domains d2a4da1 A:82-220 Ubiquitin conjugating enzyme, UBC                                                                                          SCOP domains
               CATH domains 2a4dA00 A:82-220 Ubiquitin Conjugating Enzyme                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......eeeee.........eeeeeee..........eeeeeee..........eeee................hhhhhhhhhh.....hhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------UBIQUITIN_CONJUGAT_2  PDB: A:89-214 UniProt: 15-140                                                                           ------ PROSITE
           Transcript 1 (1) 1-------------------------------------------------Exon 1.11b  PDB: A:132-173 UniProt: 58-99 Exon 1.12d  PDB: A:174-220 UniProt: 100-147     Transcript 1 (1)
           Transcript 1 (2) Exon 1.8a  PDB: A:82-131 UniProt: 8-57            ----------------------------------------------------------------------------------------- Transcript 1 (2)
                                    91       101       111       121       131       141       151       161       171       181       191       201       211         

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A4D)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UB2V1_HUMAN | Q13404)
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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    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:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0070423    nucleotide-binding oligomerization domain containing signaling pathway    Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006301    postreplication repair    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
    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:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0006282    regulation of DNA repair    Any process that modulates the frequency, rate or extent of DNA repair.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    GO:0035370    UBC13-UEV1A complex    A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-linked polyubiquitin chains and is involved in NF-kappaB activation. In humans at least, the complex comprises the ubiquitin-conjugating enzyme UBC13 and ubiquitin-conjugating enzyme variant 1A (UEV1A).
    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: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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0031371    ubiquitin conjugating enzyme complex    Any complex that possesses ubiquitin conjugating enzyme activity.
    GO:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.


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    Tyr A:149 - Pro A:150   [ RasMol ]  

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 Related Entries

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

        UB2V1_HUMAN | Q134042c2v 2hlw

(-) Related Entries Specified in the PDB File

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