UBP3/YER151C Summary Help

Standard Name UBP3 1 (see Nomenclature conflict Note)
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 (1, 3, 4, 5, 6, 7, 8 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.
Gbrowse
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
Mutant phenotypes All UBP3 Phenotype evidence and references
Classical genetics
null
reduction of function
unspecified
Large-scale survey
null
overexpression
Resources
interactions All UBP3 Interaction evidence and references
1203 total interaction(s) for 860 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 431
  • Affinity Capture-RNA: 2
  • Affinity Capture-Western: 21
  • Biochemical Activity: 8
  • 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: 526
  • Phenotypic Enhancement: 11
  • Phenotypic Suppression: 6
  • Positive Genetic: 80
  • Synthetic Growth Defect: 76
  • Synthetic Lethality: 12
  • Synthetic Rescue: 5
Resources
Expression Summary
histogram
Resources
Protein Information All UBP3 Protein evidence and references
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrV:472424 to 469686 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates		 Chromosomal
Coordinates		 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
Resources
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000953

NOMENCLATURE CONFLICT NOTE

NameRelevanceDescription
BLM10Nomenclature conflictThe name BLM3, originally referring to a genetic locus, has also been associated with YFL007W (now called BLM10) due to an error in cloning. It was later determined that blm3-1 is an allele of UBP3/YER151C.
SUMMARY PARAGRAPH for UBP3

BLM3 was identified genetically in a large screen looking for mutations conferring hypersensitivity to the drug bleomycin and radiation (9, 10). The ORF YFL007W was cloned as a multicopy suppressor of the codominant blm3-1 mutation (11). Complete deletions of the YFL007W ORF indicated that cells are hypersensitive to bleomycin and viable in the absence of the drug (11). Subsequent resequencing of the region around YFL007W indicated the presence of an additional G, resulting in the original YFL006W ORF being merged into YFL007W (12, 13). 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 (14). Thus, YFL007W was renamed BLM10 (14). The gene corresponding to the original blm3-1 mutation was later identified as UBP3 (2).

Last updated: 2008-07-22

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) 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
10) 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
11) 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
12) 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
13) Kellis M, et al.  (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54
14) Doherty K, et al.  (2004) Expression of the expanded YFL007w ORF and assignment of the gene name BLM10. Yeast 21(12):1021-3