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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
by
@meso_cacase at
DBCLS
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