UBP3/YER151C Summary Help

Standard Name UBP3 1
Systematic Name YER151C
Alias BLM3 2
Feature Type ORF, Verified
Description Ubiquitin-specific protease involved in transport and osmotic response; interacts with Bre5p to co-regulate anterograde and retrograde transport between the ER and Golgi; involved in transcription elongation in response to osmostress through phosphorylation at Ser695 by Hog1p; inhibitor of gene silencing; cleaves ubiquitin fusions but not polyubiquitin; also has mRNA binding activity; protein abundance increases in response to DNA replication stress; role in ribophagy (1, 3, 4, 5, 6, 7, 8, 9 and see Summary Paragraph)
Name Description UBiquitin-specific Protease 1
Chromosomal Location
ChrV:472424 to 469686 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All UBP3 GO evidence and references
  View Computational GO annotations for UBP3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 3 genes
Classical genetics
reduction of function
Large-scale survey
1212 total interaction(s) for 863 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 434
  • Affinity Capture-RNA: 3
  • Affinity Capture-Western: 21
  • Biochemical Activity: 10
  • Co-crystal Structure: 1
  • Co-fractionation: 1
  • Co-purification: 7
  • Reconstituted Complex: 5
  • Two-hybrid: 7

Genetic Interactions
  • Dosage Growth Defect: 1
  • Dosage Rescue: 3
  • Negative Genetic: 528
  • Phenotypic Enhancement: 11
  • Phenotypic Suppression: 7
  • Positive Genetic: 80
  • Synthetic Growth Defect: 76
  • Synthetic Lethality: 12
  • Synthetic Rescue: 5

Expression Summary
Length (a.a.) 912
Molecular Weight (Da) 101,916
Isoelectric Point (pI) 7.92
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrV:472424 to 469686 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2739 472424..469686 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000953

BLM3 was identified genetically in a large screen looking for mutations conferring hypersensitivity to the drug bleomycin and radiation (10, 11). The ORF YFL007W was cloned as a multicopy suppressor of the codominant blm3-1 mutation (12). Complete deletions of the YFL007W ORF indicated that cells are hypersensitive to bleomycin and viable in the absence of the drug (12). Subsequent resequencing of the region around YFL007W indicated the presence of an additional G, resulting in the original YFL006W ORF being merged into YFL007W (13, 14). Genetic mapping and sequencing of the expanded YFL007W ORF in the blm3-1 mutant indicated that YFL007W was an extragenic suppressor of the blm3-1 mutation (15). Thus, YFL007W was renamed BLM10 (15). The gene corresponding to the original blm3-1 mutation was later identified as UBP3 (2).

Last updated: 2008-07-22 Contact SGD

References cited on this page View Complete Literature Guide for UBP3
1) Baker RT, et al.  (1992) Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J Biol Chem 267(32):23364-75
2) McCullock S, et al.  (2006) blm3-1 Is an Allele of UBP3, a Ubiquitin Protease that Appears to Act During Transcription of Damaged DNA. J Mol Biol 363(3):660-72
3) Moazed D and Johnson D  (1996) A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86(4):667-77
4) Cohen M, et al.  (2003) Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII protein, Sec23. Nat Cell Biol 5(7):661-7
5) Cohen M, et al.  (2003) Deubiquitination, a new player in Golgi to endoplasmic reticulum retrograde transport. J Biol Chem 278(52):51989-92
6) Tsvetanova NG, et al.  (2010) Proteome-Wide Search Reveals Unexpected RNA-Binding Proteins in Saccharomyces cerevisiae.LID - e12671 [pii] PLoS One 5(9)
7) Sole C, et al.  (2011) Control of Ubp3 ubiquitin protease activity by the Hog1 SAPK modulates transcription upon osmostress.LID - 10.1038/emboj.2011.227 [doi] EMBO J ()
8) Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
9) Ossareh-Nazari B, et al.  (2014) Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy. J Cell Biol 204(6):909-17
10) Moore CW  (1980) Isolation and partial characterization of mutants of Saccharomyces cerevisiae altered in sensitivities to lethal effects of bleomycins. J Antibiot (Tokyo) 33(11):1369-75
11) Moore CW  (1991) Further characterizations of bleomycin-sensitive (blm) mutants of Saccharomyces cerevisiae with implications for a radiomimetic model. J Bacteriol 173(11):3605-8
12) Febres DE, et al.  (2001) The novel BLM3 gene encodes a protein that protects against lethal effects of oxidative damage. Cell Mol Biol (Noisy-le-grand) 47(7):1149-62
13) Robben J, et al.  (2002) Revisiting the yeast chromosome VI DNA sequence reveals a correction merging YFL007w and YFL006w to a single ORF. Yeast 19(8):699-702
14) Kellis M, et al.  (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54
15) Doherty K, et al.  (2004) Expression of the expanded YFL007w ORF and assignment of the gene name BLM10. Yeast 21(12):1021-3