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Gene Review

UBP3  -  Ubp3p

Saccharomyces cerevisiae S288c

Synonyms: Deubiquitinating enzyme 3, Ubiquitin carboxyl-terminal hydrolase 3, Ubiquitin thioesterase 3, Ubiquitin-specific-processing protease 3, YER151C
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Disease relevance of UBP3

  • Although inactive in E. coli extracts, Ubp3 was active with all of the tested ubiquitin fusions except poly-Ub when coexpressed with them in E. coli [1].

High impact information on UBP3

  • Surprisingly, the 110 kDa SIR4-binding protein is identical to UBP3, one of several previously described yeast enzymes that deubiquitinate target proteins [2].
  • Deletion of the UBP3 gene results in markedly improved silencing of genes inserted either near a telomere or at one of the silent mating type loci, indicating that UBP3 is an inhibitor of silencing [2].
  • Elevated expression of the yeast UBP3 gene, which encodes a protease that removes ubiquitin from proteins, allows mature Ty3 proteins and VLPs to accumulate in the ssa1 ssa2 mutant, suggesting that, at least under stress conditions, ubiquitination plays a role in regulating Ty3 transposition [3].
  • Deletion of UBP3 also leads to decreased targeting of Ape1p to the vacuole [4].
  • Together, these studies provide novel insights into protein recognition by NTF2-like domains and provide a molecular scaffold for understanding how Ubp3 function is regulated by Bre5 cofactor binding [5].

Biological context of UBP3

  • Ubp2 (1,264 residues), Ubp3 (912 residues), and the previously cloned Ubp1 (809 residues) are largely dissimilar except for two short regions containing Cys and His which encompass their putative active sites [1].
  • Deleting UBP3 causes phenotypes similar to those caused by blm3-1, but neither causes a general defect in DNA repair [6].
  • The ubp3 Delta mutants exhibit a potentiated response to pheromone, as measured by in vivo MAP kinase activity, transcriptional induction, and cell cycle arrest [7].

Associations of UBP3 with chemical compounds

  • Although overexpression of the yeast UBP3 gene allows VLPs to form and transposition to occur in the constitutively stressed ssa1 ssa2 strain, it does not alleviate the inhibition of these processes during stress induced by heat or ethanol [8].
  • Ubp3 is a deubiquitination enzyme and a member of a large family of cysteine proteases that cleave ubiquitin moieties from protein substrates [9].

Regulatory relationships of UBP3

  • Upon pheromone stimulation, ubp3 Delta mutants accumulate unconjugated polyubiquitin chains as well as polyubiquitinated forms of the mitogen-activated protein kinase kinase Ste7 [7].

Other interactions of UBP3

  • Using an Escherichia coli-based genetic screen, we have isolated two other yeast genes for ubiquitin-specific proteases, named UBP2 and UBP3 [1].
  • Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family [1].
  • Structural basis for interaction between the Ubp3 deubiquitinating enzyme and its Bre5 cofactor [5].
  • Also, overexpression of another yeast Dub, Ubp3, had no effect on Ste6 turnover [10].
  • The levels of Stu1p are even lower in ubp3Delta stu1-5 cells, suggesting that Ubp3p plays a role in promoting protein stability [9].


  1. Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. Baker, R.T., Tobias, J.W., Varshavsky, A. J. Biol. Chem. (1992) [Pubmed]
  2. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Moazed, D., Johnson, D. Cell (1996) [Pubmed]
  3. Cellular stress inhibits transposition of the yeast retrovirus-like element Ty3 by a ubiquitin-dependent block of virus-like particle formation. Menees, T.M., Sandmeyer, S.B. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  4. Atg19p ubiquitination and the cytoplasm to vacuole trafficking pathway in yeast. Baxter, B.K., Abeliovich, H., Zhang, X., Stirling, A.G., Burlingame, A.L., Goldfarb, D.S. J. Biol. Chem. (2005) [Pubmed]
  5. Structural basis for interaction between the Ubp3 deubiquitinating enzyme and its Bre5 cofactor. Li, K., Zhao, K., Ossareh-Nazari, B., Da, G., Dargemont, C., Marmorstein, R. J. Biol. Chem. (2005) [Pubmed]
  6. blm3-1 Is an Allele of UBP3, a Ubiquitin Protease that Appears to Act During Transcription of Damaged DNA. McCullock, S., Kinard, T., McCullough, L., Formosa, T. J. Mol. Biol. (2006) [Pubmed]
  7. Pheromone-dependent ubiquitination of the mitogen-activated protein kinase kinase Ste7. Wang, Y., Dohlman, H.G. J. Biol. Chem. (2002) [Pubmed]
  8. Thermal blockage of viruslike particle formation for the yeast retrotransposon Ty3 reveals differences in the cellular stress response. Sadeghi, N., Rütz, M.L., Menees, T.M. Arch. Virol. (2001) [Pubmed]
  9. The yeast ubiquitin protease, Ubp3p, promotes protein stability. Brew, C.T., Huffaker, T.C. Genetics (2002) [Pubmed]
  10. The deubiquitinating enzyme Ubp1 affects sorting of the ATP-binding cassette-transporter Ste6 in the endocytic pathway. Schmitz, C., Kinner, A., Kölling, R. Mol. Biol. Cell (2005) [Pubmed]
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