UPF3B

UPF3 regulator of nonsense transcripts homolog B (yeast)

PDB rendering based on 1uw4.

Available structures
PDB	1UW4, 2XB2

Identifiers

Symbols

UPF3B; HUPF3B; MRXS14; RENT3B; UPF3X

External IDs

OMIM: 300298 MGI: 1915384 HomoloGene: 11307 GeneCards: UPF3B Gene

Gene Ontology
Molecular function	• nucleotide binding • mRNA binding • nucleocytoplasmic transporter activity • protein binding
Cellular component	• nucleus • nucleoplasm • cytoplasm • cytoplasm • cytosol • exon-exon junction complex • exon-exon junction complex
Biological process	• nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear-transcribed mRNA catabolic process, nonsense-mediated decay • nuclear mRNA splicing, via spliceosome • transcription from RNA polymerase II promoter • termination of RNA polymerase II transcription • mRNA export from nucleus • transport • nucleocytoplasmic transport • RNA splicing • gene expression • mRNA 3'-end processing • positive regulation of translation
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

n/a

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr X:
118.97 – 118.99 Mb

Chr X:
34.63 – 34.65 Mb

PubMed search

[1]

[2]

Regulator of nonsense transcripts 3B is a protein that in humans is encoded by the UPF3B gene.^[1]^[2]^[3]

This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene.^[3]

Interactions

UPF3B has been shown to interact with UPF2^[2]^[4]^[5]^[6] and UPF1.^[2]^[5]^[7]

References

^ Serin G, Gersappe A, Black JD, Aronoff R, Maquat LE (Jan 2001). "Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4)". Mol Cell Biol 21 (1): 209–23. doi:10.1128/MCB.21.1.209-223.2001. PMC 88795. PMID 11113196. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=88795.
^ ^a ^b ^c Lykke-Andersen J, Shu MD, Steitz JA (Feb 2001). "Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon". Cell 103 (7): 1121–31. doi:10.1016/S0092-8674(00)00214-2. PMID 11163187.
^ ^a ^b "Entrez Gene: UPF3B UPF3 regulator of nonsense transcripts homolog B (yeast)". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=65109.
^ Lehner, Ben; Sanderson Christopher M (Jul. 2004). "A protein interaction framework for human mRNA degradation". Genome Res. (United States) 14 (7): 1315–23. doi:10.1101/gr.2122004. ISSN 1088-9051. PMC 442147. PMID 15231747. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=442147.
^ ^a ^b Lejeune, Fabrice; Li Xiaojie, Maquat Lynne E (Sep. 2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities". Mol. Cell (United States) 12 (3): 675–87. doi:10.1016/S1097-2765(03)00349-6. ISSN 1097-2765. PMID 14527413.
^ Lykke-Andersen, Jens (Dec. 2002). "Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay". Mol. Cell. Biol. (United States) 22 (23): 8114–21. doi:10.1128/MCB.22.23.8114-8121.2002. ISSN 0270-7306. PMC 134073. PMID 12417715. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=134073.
^ Schell, Thomas; Köcher Thomas, Wilm Matthias, Seraphin Bertrand, Kulozik Andreas E, Hentze Matthias W (Aug. 2003). "Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells". Biochem. J. (England) 373 (Pt 3): 775–83. doi:10.1042/BJ20021920. ISSN 0264-6021. PMC 1223536. PMID 12723973. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1223536.

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Kim VN, Kataoka N, Dreyfuss G (2001). "Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex.". Science 293 (5536): 1832–6. doi:10.1126/science.1062829. PMID 11546873.
Lykke-Andersen J, Shu MD, Steitz JA (2001). "Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1.". Science 293 (5536): 1836–9. doi:10.1126/science.1062786. PMID 11546874.
Lejeune F, Ishigaki Y, Li X, Maquat LE (2002). "The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling.". EMBO J. 21 (13): 3536–45. doi:10.1093/emboj/cdf345. PMC 126094. PMID 12093754. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=126094.
Lykke-Andersen J (2003). "Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay.". Mol. Cell. Biol. 22 (23): 8114–21. doi:10.1128/MCB.22.23.8114-8121.2002. PMC 134073. PMID 12417715. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=134073.
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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=139241.
Chiu SY, Serin G, Ohara O, Maquat LE (2003). "Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1.". RNA 9 (1): 77–87. doi:10.1261/rna.2137903. PMC 1370372. PMID 12554878. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1370372.
Gehring NH, Neu-Yilik G, Schell T, et al. (2003). "Y14 and hUpf3b form an NMD-activating complex.". Mol. Cell 11 (4): 939–49. doi:10.1016/S1097-2765(03)00142-4. PMID 12718880.
Schell T, Köcher T, Wilm M, et al. (2003). "Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells.". Biochem. J. 373 (Pt 3): 775–83. doi:10.1042/BJ20021920. PMC 1223536. PMID 12723973. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1223536.
Lejeune F, Li X, Maquat LE (2003). "Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities.". Mol. Cell 12 (3): 675–87. doi:10.1016/S1097-2765(03)00349-6. PMID 14527413.
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.
Kadlec J, Izaurralde E, Cusack S (2004). "The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.". Nat. Struct. Mol. Biol. 11 (4): 330–7. doi:10.1038/nsmb741. PMID 15004547.
Lehner B, Sanderson CM (2004). "A protein interaction framework for human mRNA degradation.". Genome Res. 14 (7): 1315–23. doi:10.1101/gr.2122004. PMC 442147. PMID 15231747. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=442147.
Andersen JS, Lam YW, Leung AK, et al. (2005). "Nucleolar proteome dynamics.". Nature 433 (7021): 77–83. doi:10.1038/nature03207. PMID 15635413.
Kim YK, Furic L, Desgroseillers L, Maquat LE (2005). "Mammalian Staufen1 recruits Upf1 to specific mRNA 3'UTRs so as to elicit mRNA decay.". Cell 120 (2): 195–208. doi:10.1016/j.cell.2004.11.050. PMID 15680326.
Gehring NH, Kunz JB, Neu-Yilik G, et al. (2005). "Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements.". Mol. Cell 20 (1): 65–75. doi:10.1016/j.molcel.2005.08.012. PMID 16209946.
Kunz JB, Neu-Yilik G, Hentze MW, et al. (2006). "Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation.". RNA 12 (6): 1015–22. doi:10.1261/rna.12506. PMC 1464862. PMID 16601204. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1464862.

PDB gallery

1uw4: THE STRUCTURAL BASIS OF THE INTERACTION BETWEEN NONSENSE MEDIATED DECAY FACTORS UPF2 AND UPF3

UPF3B

Interactions

References

Further reading