Ube2d3

Ubiquitin-conjugating enzyme E2D 3

PDB rendering based on 1ur6.

Available structures

Ortholog search: PDBe, RCSB

List of PDB id codes
1X23, 2FUH, 3L1Z, 3RPG

Identifiers

Symbols

UBE2D3; E2(17)KB3; UBC4/5; UBCH5C

External IDs

OMIM: 602963 MGI: 1913355 HomoloGene: 123914 GeneCards: UBE2D3 Gene

EC number

6.3.2.19

Gene Ontology
Molecular function	• nucleotide binding • ubiquitin-protein ligase activity • protein binding • ATP binding • ligase activity • acid-amino acid ligase activity
Cellular component	• nucleoplasm • endosome • cytosol • plasma membrane • endosome membrane
Biological process	• protein polyubiquitination • DNA repair • protein modification process • ubiquitin-dependent protein catabolic process • protein monoubiquitination • apoptotic process • transforming growth factor beta receptor signaling pathway • protein ubiquitination • protein ubiquitination • BMP signaling pathway • negative regulation of type I interferon production • proteasomal ubiquitin-dependent protein catabolic process • innate immune response • protein K48-linked ubiquitination • protein K11-linked ubiquitination
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 4:
103.72 – 103.79 Mb

Chr 3:
135.1 – 135.13 Mb

PubMed search

[1]

[2]

Ubiquitin-conjugating enzyme E2 D3 is a protein that in humans is encoded by the UBE2D3 gene.^[1]^[2]

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.^[2]

Interactions [link]

UBE2D3 has been shown to interact with NEDD4.^[3]^[4]

References [link]

^ Jensen JP, Bates PW, Yang M, Vierstra RD, Weissman AM (Jan 1996). "Identification of a family of closely related human ubiquitin conjugating enzymes". J Biol Chem 270 (51): 30408–14. DOI:10.1074/jbc.270.51.30408. PMID 8530467.
^ ^a ^b "Entrez Gene: UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)". https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=7323.
^ Anan, T; Nagata Y, Koga H, Honda Y, Yabuki N, Miyamoto C, Kuwano A, Matsuda I, Endo F, Saya H, Nakao M (Nov. 1998). "Human ubiquitin-protein ligase Nedd4: expression, subcellular localization and selective interaction with ubiquitin-conjugating enzymes". Genes Cells (ENGLAND) 3 (11): 751–63. DOI:10.1046/j.1365-2443.1998.00227.x. ISSN 1356-9597. PMID 9990509.
^ Wang, Xinjiang; Shi Yuji, Wang Junru, Huang Guochang, Jiang Xuejun (Sep. 2008). "Crucial role of the C-terminus of PTEN in antagonizing NEDD4-1-mediated PTEN ubiquitination and degradation". Biochem. J. (England) 414 (2): 221–9. DOI:10.1042/BJ20080674. PMID 18498243.

Further reading [link]

Scheffner M, Huibregtse JM, Howley PM (1994). "Identification of a human ubiquitin-conjugating enzyme that mediates the E6-AP-dependent ubiquitination of p53.". Proc. Natl. Acad. Sci. U.S.A. 91 (19): 8797–801. DOI:10.1073/pnas.91.19.8797. PMC 44693. PMID 8090726. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=44693.
Rogakou EP, Pilch DR, Orr AH, et al. (1998). "DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139.". J. Biol. Chem. 273 (10): 5858–68. DOI:10.1074/jbc.273.10.5858. PMID 9488723.
Anan T, Nagata Y, Koga H, et al. (1999). "Human ubiquitin-protein ligase Nedd4: expression, subcellular localization and selective interaction with ubiquitin-conjugating enzymes.". Genes Cells 3 (11): 751–63. DOI:10.1046/j.1365-2443.1998.00227.x. PMID 9990509.
Gonen H, Bercovich B, Orian A, et al. (1999). "Identification of the ubiquitin carrier proteins, E2s, involved in signal-induced conjugation and subsequent degradation of IkappaBalpha.". J. Biol. Chem. 274 (21): 14823–30. DOI:10.1074/jbc.274.21.14823. PMID 10329681.
Orian A, Gonen H, Bercovich B, et al. (2000). "SCF(beta)(-TrCP) ubiquitin ligase-mediated processing of NF-kappaB p105 requires phosphorylation of its C-terminus by IkappaB kinase.". EMBO J. 19 (11): 2580–91. DOI:10.1093/emboj/19.11.2580. PMC 212749. PMID 10835356. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=212749.
Coleman CS, Pegg AE (2001). "Polyamine analogues inhibit the ubiquitination of spermidine/spermine N1-acetyltransferase and prevent its targeting to the proteasome for degradation.". Biochem. J. 358 (Pt 1): 137–45. DOI:10.1042/0264-6021:3580137. PMC 1222041. PMID 11485561. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1222041.
Chen A, Kleiman FE, Manley JL, et al. (2002). "Autoubiquitination of the BRCA1*BARD1 RING ubiquitin ligase.". J. Biol. Chem. 277 (24): 22085–92. DOI:10.1074/jbc.M201252200. PMID 11927591.
Obin M, Lee BY, Meinke G, et al. (2003). "Ubiquitylation of the transducin betagamma subunit complex. Regulation by phosducin.". J. Biol. Chem. 277 (46): 44566–75. DOI:10.1074/jbc.M205308200. PMID 12215439.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. DOI:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.
Takeyama K, Aguiar RC, Gu L, et al. (2003). "The BAL-binding protein BBAP and related Deltex family members exhibit ubiquitin-protein isopeptide ligase activity.". J. Biol. Chem. 278 (24): 21930–7. DOI:10.1074/jbc.M301157200. PMID 12670957.
Brzovic PS, Keeffe JR, Nishikawa H, et al. (2003). "Binding and recognition in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex.". Proc. Natl. Acad. Sci. U.S.A. 100 (10): 5646–51. DOI:10.1073/pnas.0836054100. PMC 156255. PMID 12732733. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=156255.
Tang ED, Wang CY, Xiong Y, Guan KL (2003). "A role for NF-kappaB essential modifier/IkappaB kinase-gamma (NEMO/IKKgamma) ubiquitination in the activation of the IkappaB kinase complex by tumor necrosis factor-alpha.". J. Biol. Chem. 278 (39): 37297–305. DOI:10.1074/jbc.M303389200. PMID 12867425.
Subramaniam V, Li H, Wong M, et al. (2003). "The RING-H2 protein RNF11 is overexpressed in breast cancer and is a target of Smurf2 E3 ligase.". Br. J. Cancer 89 (8): 1538–44. DOI:10.1038/sj.bjc.6601301. PMC 2394340. PMID 14562029. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2394340.
Lehner B, Semple JI, Brown SE, et al. (2004). "Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region.". Genomics 83 (1): 153–67. DOI:10.1016/S0888-7543(03)00235-0. PMID 14667819.
Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs.". Nat. Genet. 36 (1): 40–5. DOI:10.1038/ng1285. PMID 14702039.
Saville MK, Sparks A, Xirodimas DP, et al. (2004). "Regulation of p53 by the ubiquitin-conjugating enzymes UbcH5B/C in vivo.". J. Biol. Chem. 279 (40): 42169–81. DOI:10.1074/jbc.M403362200. PMID 15280377.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).". Genome Res. 14 (10B): 2121–7. DOI:10.1101/gr.2596504. PMC 528928. PMID 15489334. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=528928.
Rual JF, Venkatesan K, Hao T, et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network.". Nature 437 (7062): 1173–8. DOI:10.1038/nature04209. PMID 16189514.
Kimura K, Wakamatsu A, Suzuki Y, et al. (2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.". Genome Res. 16 (1): 55–65. DOI:10.1101/gr.4039406. PMC 1356129. PMID 16344560. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1356129.

PDB gallery

1ur6: NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX

1w4u: NMR SOLUTION STRUCTURE OF THE UBIQUITIN CONJUGATING ENZYME UBCH5B

1x23: Crystal structure of ubch5c

1z2u: The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

2c4o: CRYSTAL STRUCTURE OF HUMAN UBIQUITIN-CONJUGATING ENZYME UBCH5B

2esk: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type

2eso: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala

2esp: Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala

2esq: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly

2fuh: Solution Structure of the UbcH5c/Ub Non-covalent Complex

Posttranslational modification

Chaperones/
protein folding

Heat shock proteins/ Chaperonins	Hsp10/GroES (Early pregnancy factor) · Hsp27 · Hsp47 · HSP60/GroEL Hsp40/DnaJ (A1, A2, A3, B1, B2, B11, B4, B6, B9, C1, C3, C5, C6, C7, C10, C11, C13, C14, C19) Hsp70 (1A, 1B, 1L, 2, 4, 4L, 5, 6, 7, 8, 9, 12A, 14) Hsp90 (α₁, α₂, β, ER, TRAP1)

Other	Alpha crystallin · Clusterin · Survival of motor neuron (SMN1, SMN2)

Protein targeting

Signal peptide

Ubiquitin

E1 Ubiquitin-activating enzyme (UBA1, UBA2, UBA3, UBA5, UBA6, UBA7, ATG7, NAE1, SAE1)

E2 Ubiquitin-conjugating enzyme (A • B • C • D1, D2, D3 • E1, E2, E3 • G1, G2 • H • I • J1, J2 • K • L1, L2, L3, L4, L6 • M • N • O • Q1, Q2 • R1 (CDC34), R2 • S • V1, V2 • Z)

E3 Ubiquitin ligase (VHL, Cullin, CBL, MDM2, FANCL, UBR1)

Deubiquitinating enzyme: Ataxin 3 • USP6 • CYLD

ATG3 • BIRC6 • UFC1

Other

SUMO protein

see also posttranslational modification disorders
B bsyn: dna (repl, cycl, reco, repr) · tscr (fact, tcrg, nucl, rnat, rept, ptts) · tltn (risu, pttl, nexn) · dnab, rnab/runp · stru (domn, 1°, 2°, 3°, 4°)

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Interactions [link]

References [link]

Further reading [link]

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