2024-04-18 11:28:22, GGRNA : RefSeq release 60 (20130726)
LOCUS NM_003340 3976 bp mRNA linear PRI 08-JUL-2013 DEFINITION Homo sapiens ubiquitin-conjugating enzyme E2D 3 (UBE2D3), transcript variant 1, mRNA. ACCESSION NM_003340 VERSION NM_003340.6 GI:514825582 KEYWORDS RefSeq. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 3976) AUTHORS Soss,S.E., Klevit,R.E. and Chazin,W.J. TITLE Activation of UbcH5c Ub is the result of a shift in interdomain motions of the conjugate bound to U-box E3 ligase E4B JOURNAL Biochemistry 52 (17), 2991-2999 (2013) PUBMED 23550736 REMARK GeneRIF: although a reduction in interdomain dynamics of UbcH5c~Ub is observed upon binding to E4B, Ub retains an extensive degree of flexibility REFERENCE 2 (bases 1 to 3976) AUTHORS Bentley,M.L., Corn,J.E., Dong,K.C., Phung,Q., Cheung,T.K. and Cochran,A.G. TITLE Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex JOURNAL EMBO J. 30 (16), 3285-3297 (2011) PUBMED 21772249 REMARK GeneRIF: The crystal structure of a complex of the Bmi1/Ring1b RING-RING heterodimer & UbcH5c shows that UbcH5c interacts with Ring1b only. Publication Status: Online-Only REFERENCE 3 (bases 1 to 3976) AUTHORS Pan,Y., Ma,J., Zhang,W., Wang,Y., Wang,Y., Zhang,H., Wang,M., Zhang,Z. and Wang,L. TITLE Replication of two novel susceptibility loci for non-syndromic orofacial clefts in a Chinese population JOURNAL Oral Dis 17 (3), 304-308 (2011) PUBMED 20860768 REMARK GeneRIF: Observational study of gene-disease association. (HuGE Navigator) REFERENCE 4 (bases 1 to 3976) AUTHORS Pruneda,J.N., Stoll,K.E., Bolton,L.J., Brzovic,P.S. and Klevit,R.E. TITLE Ubiquitin in motion: structural studies of the ubiquitin-conjugating enzyme approximately ubiquitin conjugate JOURNAL Biochemistry 50 (10), 1624-1633 (2011) PUBMED 21226485 REMARK GeneRIF: UbcH5c approximately Ub conjugate populates an array of extended conformations, and the population of Ubc13 approximately Ub conjugates favors a closed conformation in which the hydrophobic surface of Ub faces helix 2 of Ubc13 REFERENCE 5 (bases 1 to 3976) AUTHORS Benirschke,R.C., Thompson,J.R., Nomine,Y., Wasielewski,E., Juranic,N., Macura,S., Hatakeyama,S., Nakayama,K.I., Botuyan,M.V. and Mer,G. TITLE Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4 JOURNAL Structure 18 (8), 955-965 (2010) PUBMED 20696396 REMARK GeneRIF: determined structures of E4B U box free and bound to UbcH5c and Ubc4 E2s; findings show E4B U box is a monomer stabilized by a network of hydrogen bonds; findings suggest allosteric regulation of UbcH5c and Ubc4 by E4B U box REFERENCE 6 (bases 1 to 3976) AUTHORS Gonen,H., Bercovich,B., Orian,A., Carrano,A., Takizawa,C., Yamanaka,K., Pagano,M., Iwai,K. and Ciechanover,A. TITLE Identification of the ubiquitin carrier proteins, E2s, involved in signal-induced conjugation and subsequent degradation of IkappaBalpha JOURNAL J. Biol. Chem. 274 (21), 14823-14830 (1999) PUBMED 10329681 REFERENCE 7 (bases 1 to 3976) AUTHORS Anan,T., Nagata,Y., Koga,H., Honda,Y., Yabuki,N., Miyamoto,C., Kuwano,A., Matsuda,I., Endo,F., Saya,H. and Nakao,M. TITLE Human ubiquitin-protein ligase Nedd4: expression, subcellular localization and selective interaction with ubiquitin-conjugating enzymes JOURNAL Genes Cells 3 (11), 751-763 (1998) PUBMED 9990509 REFERENCE 8 (bases 1 to 3976) AUTHORS Rogakou,E.P., Pilch,D.R., Orr,A.H., Ivanova,V.S. and Bonner,W.M. TITLE DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139 JOURNAL J. Biol. Chem. 273 (10), 5858-5868 (1998) PUBMED 9488723 REFERENCE 9 (bases 1 to 3976) AUTHORS Jensen,J.P., Bates,P.W., Yang,M., Vierstra,R.D. and Weissman,A.M. TITLE Identification of a family of closely related human ubiquitin conjugating enzymes JOURNAL J. Biol. Chem. 270 (51), 30408-30414 (1995) PUBMED 8530467 REFERENCE 10 (bases 1 to 3976) AUTHORS Scheffner,M., Huibregtse,J.M. and Howley,P.M. TITLE Identification of a human ubiquitin-conjugating enzyme that mediates the E6-AP-dependent ubiquitination of p53 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 91 (19), 8797-8801 (1994) PUBMED 8090726 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from BM750658.1, DA557036.1, BC003395.1, AC018797.4 and BM967209.1. On Jun 26, 2013 this sequence version replaced gi:259155308. Summary: The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme functions in the ubiquitination of the tumor-suppressor protein p53, which is induced by an E3 ubiquitin-protein ligase. Multiple spliced transcript variants have been found for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]. Transcript Variant: This variant (1) encodes the predominant isoform (1). Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC037894.2, AL534425.3 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025084, ERS025088 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: complete on the 3' end. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-230 BM750658.1 1-230 231-638 DA557036.1 158-565 639-1754 BC003395.1 319-1434 1755-3741 AC018797.4 91225-93211 c 3742-3976 BM967209.1 193-427 FEATURES Location/Qualifiers source 1..3976 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="4" /map="4q24" gene 1..3976 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="ubiquitin-conjugating enzyme E2D 3" /db_xref="GeneID:7323" /db_xref="HGNC:12476" /db_xref="MIM:602963" exon 1..357 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" exon 358..509 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" misc_feature 459..461 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="upstream in-frame stop codon" CDS 486..929 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /EC_number="6.3.2.19" /note="isoform 1 is encoded by transcript variant 1; ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5); ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast); ubiquitin-conjugating enzyme E2-17 kDa 3; E2(17)KB 3; ubiquitin-protein ligase D3; ubiquitin carrier protein D3; ubiquitin-conjugating enzyme E2(17)KB 3; PRO2116" /codon_start=1 /product="ubiquitin-conjugating enzyme E2 D3 isoform 1" /protein_id="NP_003331.1" /db_xref="GI:4507777" /db_xref="CCDS:CCDS3660.1" /db_xref="GeneID:7323" /db_xref="HGNC:12476" /db_xref="MIM:602963" /translation="
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM
" misc_feature 495..911 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin...; Region: UBCc; cd00195" /db_xref="CDD:238117" misc_feature order(495..497,666..671,768..773) /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="E3 interaction residues; other site" /db_xref="CDD:238117" misc_feature order(699..704,714..719,723..725,735..743,747..752, 762..767,774..776,789..791,798..800,807..809,816..821, 825..827,831..836) /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="Ub thioester intermediate interaction residues; other site" /db_xref="CDD:238117" misc_feature 738..740 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /note="active site cysteine" /db_xref="CDD:238117" exon 510..573 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" exon 574..605 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" STS 598..822 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /standard_name="RH125441" /db_xref="UniSTS:162261" exon 606..683 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" exon 684..789 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" exon 790..883 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" exon 884..3961 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /inference="alignment:Splign:1.39.8" STS 2015..2122 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /standard_name="G19979" /db_xref="UniSTS:35899" STS 2015..2122 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /standard_name="RH16693" /db_xref="UniSTS:84034" STS 2517..2617 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" /standard_name="SHGC-37168" /db_xref="UniSTS:62357" polyA_signal 3939..3944 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" polyA_site 3961 /gene="UBE2D3" /gene_synonym="E2(17)KB3; UBC4/5; UBCH5C" ORIGIN
accaagtgaggaaactgggggacgctgtggggaggggcgtggggctggatcgcgcagcggctgcttcctttaccttcctcccatggtctccttccggttctcgatgcttctctgagcctaagggtttccgccactcgttcaccctccccccagctcatgatcctcctccctcccccgccctcctggtccaatctccgatctgtttagtaagaaggtgctgttccgagaagaaggaaaagggcttgacacgtattcactcggccccggacgtgggaagcaagccgtctggcttcggcctcacatcggtcttgtgctcgggacggcggcgttggcggactgatccgcggcggtgaagaggcgcctgtgtctggcagagctggtgtgagacgagacaatcctgccccgccgccgggataatcaagagttttggccggacctttgagcatacaccgagagagtgaggagccagacgacaagcacacactatggcgctgaaacggattaataaggaacttagtgatttggcccgtgaccctccagcacaatgttctgcaggtccagttggggatgatatgtttcattggcaagccacaattatgggacctaatgacagcccatatcaaggcggtgtattctttttgacaattcattttcctacagactaccccttcaaaccacctaaggttgcatttacaacaagaatttatcatccaaatattaacagtaatggcagcatttgtctcgatattctaagatcacagtggtcgcctgctttaacaatttctaaagttcttttatccatttgttcactgctatgtgatccaaacccagatgaccccctagtgccagagattgcacggatctataaaacagacagagataagtacaacagaatatctcgggaatggactcagaagtatgccatgtgatgctaccttaaagtcagaataacctgcattatagctggaataaactttaaattactgttccttttttgattttcttatccggctgctcccctatcagacctcatcttttttaattttattttttgtttacctccctccattcattcacatgctcatctgagaagacttaagttcttccagctttggacaataactgcttttagaaactgtaaagtagttacaagagaacagttgcccaagactcagaatttttaaaaaaaaaaatggagcatgtgtattatgtggccaatgtcttcactctaacttggttatgagactaaaaccattcctcactgctctaacatgctgaagaaatcatctgagggggagggagatggatgctcagttgtcacatcaaaggatacagcattattctagcagcatccattcttgtttaagccttccactgttagagatttgaggttacatgatatgctttatgctcataactgatgtggctggagaattggtattgaatttatagcatcagcagaacagaaaatgtgatgtattttatgcatgtcaataaaggaatgacctgttcttgttctacagagaatggaaattggaagtcaaacaccctttgtattccaaaatagggtctcaaacattttgtaattttcatttaaattgttaggaggcttggagctattagttaatctatcttccaatacactgtttaatatagcactgaataaatgatgcaagttgtcaatggatgagtgatcaactaatagctctgctagtaattgatttatttttcttcaataaagttgcataaaccaatgagttagctgcctggattaatcagtatgggaaacaatcttttgtaaatgcaaagctgttttttgtatatactgttgggatttgcttcattgtttgacatcaaatgatgatgtaaagttcgaaagagtgaatattttgccatgttcagttaaagtgcacagtctgttacaggttgacacattgcttgacctgatttatgcagaattaataagctatttggatagtgtagctttaatgtgctgcacatgatactggcagccctagagttcatagatggacttttgggacccagcagttttgaaatgtgtttatggagtttaagaaatttattttccaggtgcagcccctgtctaactgaaatttctcttcaccttgtacacttgacagctgaaaaaaaacaacatgggagtaataatgggtcaaaatttgcaaaataaagtactgttttggtgtgggagttgtcatgaggctgtgttgaagtgacttatctatgtgggatattgagtatccattgaaatggatttgttcagccatttacattaatgagcatttaaatgcaacagatatcatttcaggtgacttaacatgaatgaataaaagtcaatgctattggattgttttttgtttgacaagtgctatctgtgccactgatttaacttctgtagtaacaagggcattaccattcttcacctttcctaattctgatcccatagttttacatttttcctgtttattttgattttgttcactgctttatttcttaaagttctagcacatctgtgactcctccacttccacatttttgcactgcttacacttacgtgcaatcttattccttgtctgcacacacatgtggaaagctagaaataaatgttaaaacttactttttataaacattttaatatgtagtttggacatgatttattgacttaaggttcttctctaaactggaagtgaaatgcatgccttctgaagatgttctggctttgttaattctgtaatcatttcattggggaaaaaaccagctacgcagtttttccaatgagtgaattttttcattttgtgttttgcttaaaacggctccttcagggtagatgtcatactgcataacttttttggattcaaattatgaatgagaaattagttaacattctgctccacaaggtaagaaaaactgctctttggctctattttcaaaattacttctgagatgcatatagtctcaaaataacagctttagtaggcatatcacttcttgaaagccaaacatgagtgtaagacacttttatgaaacacggtggatccctaactggctttcaaattgacctttatagccttagacaacccttaggtatttacggagatgacttctttgattgtcataacaattagtggatgtgtccagttctctgtatctttgacttgatgctttatacatcatttcatttgttgcttctaagggaataagccatagaggcttctccaggtttaaaagaacagtaaagtacctggaaaaccaacatttttgaatgtatggacactggacatgagatatgtacaatgaaatcttaaaagaatctaagaatttgccctctttgccccactccacccagtaatttgacattactagtgccatgtataggacccaactgagtattagaatcagttttgactatgtctttgtatttcctaaatcttttaatgcataaaccgaattagggtccagttggcctgttaatggtaaatttacattttaaatgactcagtttgtttttcctgggcgagtttgcaatgtgataatcagattttttaaaactgattaatttgctttcttgtgtgggtgtactcacattttaaagtatgaaccacagttaactagtggtctcaggggtagtgaaacactcacttttttttttgtttgtttttttttgtttgttgaaatggcttagttgaagtatacttaaggtactgatcatgctgtgttagtaatttgggcggggaggggggtaactcagccatgttttgtgttggcataacaaaactgttaatgattgttgattacacttttaagtgaatttgtcttttatgaggaacccagtgcaagtcactaaatattgtctaatagtgacatctgcataagacttgtaatagctgaagttaattgagcttaaaggaattgttaccattaaagtctgtgtttaaagacaaaaaaaaaaaaaaaa
//
ANNOTATIONS from NCBI Entrez Gene (20130726): GeneID:7323 -> Molecular function: GO:0004842 [ubiquitin-protein ligase activity] evidence: IDA GeneID:7323 -> Molecular function: GO:0005515 [protein binding] evidence: IPI GeneID:7323 -> Molecular function: GO:0005524 [ATP binding] evidence: IEA GeneID:7323 -> Biological process: GO:0000122 [negative regulation of transcription from RNA polymerase II promoter] evidence: TAS GeneID:7323 -> Biological process: GO:0000209 [protein polyubiquitination] evidence: IDA GeneID:7323 -> Biological process: GO:0002224 [toll-like receptor signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0002756 [MyD88-independent toll-like receptor signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0006281 [DNA repair] evidence: IEA GeneID:7323 -> Biological process: GO:0006351 [transcription, DNA-dependent] evidence: TAS GeneID:7323 -> Biological process: GO:0006367 [transcription initiation from RNA polymerase II promoter] evidence: TAS GeneID:7323 -> Biological process: GO:0006464 [cellular protein modification process] evidence: TAS GeneID:7323 -> Biological process: GO:0006511 [ubiquitin-dependent protein catabolic process] evidence: TAS GeneID:7323 -> Biological process: GO:0006513 [protein monoubiquitination] evidence: IDA GeneID:7323 -> Biological process: GO:0006915 [apoptotic process] evidence: IEA GeneID:7323 -> Biological process: GO:0007179 [transforming growth factor beta receptor signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0010467 [gene expression] evidence: TAS GeneID:7323 -> Biological process: GO:0016567 [protein ubiquitination] evidence: IDA GeneID:7323 -> Biological process: GO:0030509 [BMP signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0032480 [negative regulation of type I interferon production] evidence: TAS GeneID:7323 -> Biological process: GO:0034138 [toll-like receptor 3 signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0034142 [toll-like receptor 4 signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0035666 [TRIF-dependent toll-like receptor signaling pathway] evidence: TAS GeneID:7323 -> Biological process: GO:0043161 [proteasomal ubiquitin-dependent protein catabolic process] evidence: IDA GeneID:7323 -> Biological process: GO:0045087 [innate immune response] evidence: TAS GeneID:7323 -> Biological process: GO:0061418 [regulation of transcription from RNA polymerase II promoter in response to hypoxia] evidence: TAS GeneID:7323 -> Biological process: GO:0070936 [protein K48-linked ubiquitination] evidence: IDA GeneID:7323 -> Biological process: GO:0070979 [protein K11-linked ubiquitination] evidence: IDA GeneID:7323 -> Biological process: GO:0071456 [cellular response to hypoxia] evidence: TAS GeneID:7323 -> Cellular component: GO:0005654 [nucleoplasm] evidence: TAS GeneID:7323 -> Cellular component: GO:0005829 [cytosol] evidence: TAS GeneID:7323 -> Cellular component: GO:0005886 [plasma membrane] evidence: IEA GeneID:7323 -> Cellular component: GO:0010008 [endosome membrane] evidence: IEA ANNOTATIONS from NCBI Entrez Gene (20130726): NP_003331 -> EC 6.3.2.19
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