UBP3 mRNA-binding ubiquitin-specific protease UBP3 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: UBP3
Official Full Name: mRNA-binding ubiquitin-specific protease UBP3
Primary source: SGD:S000000953
Locus tag: YER151C
See related: AllianceGenome:SGD:S000000953; FungiDB:YER151C; VEuPathDB:YER151C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: BLM3
Summary: Enables cysteine-type deubiquitinase activity and mRNA binding activity. Involved in several processes, including protein retention in Golgi apparatus; regulation of ER to Golgi vesicle-mediated transport; and ribophagy. Located in cytoplasm. Part of Ubp3-Bre5 deubiquitination complex. Orthologous to human USP10 (ubiquitin specific peptidase 10). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See UBP3 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 1

Sequence:: Chromosome: V; NC_001137.3 (469686..472424, complement)

Chromosome V - NC_001137.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001137.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting.
Title: The deubiquitinase Ubp3/Usp10 constrains glucose-mediated mitochondrial repression via phosphate budgeting.
Deubiquitinase Ubp3 enhances the proteasomal degradation of key enzymes in sterol homeostasis.
Title: Deubiquitinase Ubp3 enhances the proteasomal degradation of key enzymes in sterol homeostasis.
A novel mechanism for the retention of Golgi membrane proteins mediated by the Bre5p/Ubp3p deubiquitinase complex.
Title: A novel mechanism for the retention of Golgi membrane proteins mediated by the Bre5p/Ubp3p deubiquitinase complex.
The results indicated that two different Ubp3 and Ubx2 complexes independently regulate mitochondrial fusion and Fzo1 turnover.
Title: Two Cdc48 cofactors Ubp3 and Ubx2 regulate mitochondrial morphology and protein turnover.
Ubp2 and Ubp3 deubiquitinases are required for the proteasomal degradation of cytosolic misfolded proteins targeted by Rsp5 after heat-shock
Title: Deubiquitinase activity is required for the proteasomal degradation of misfolded cytosolic proteins upon heat-stress.
Here, the authors identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex.
Title: RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit.
Ubp3 is essential for proper proteasome function in euploid cells, and deletion of this deubiquitinase leads to further proteasome-mediated proteotoxicity in aneuploid yeast
Title: The pleiotropic deubiquitinase Ubp3 confers aneuploidy tolerance.
We show that PRO1 genetically interacts with UBP3, which encodes ubiquitin-specific protease, and is required for selective autophagy of ribosomes (ribophagy).
Title: γ-Glutamyl kinase is involved in selective autophagy of ribosomes in Saccharomyces cerevisiae.
Data suggest regulated process for removal of proteasomes upon nitrogen starvation; autophagy involves separate processes for dissociation and nuclear export of core (PRE2) and regulatory (RPN1) proteins; only core protein autophagy depends on UBP3.
Title: Starvation Induces Proteasome Autophagy with Different Pathways for Core and Regulatory Particles.
Taken together, these results demonstrate that Rck1 promotes S. cerevisiae pseudohyphal growth via the activation of Ubp3 phosphorylation.
Title: Rck1 promotes pseudohyphal growth via the activation of Ubp3 phosphorylation in Saccharomyces cerevisiae.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables cysteine-type deubiquitinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cysteine-type peptidase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in protein deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein deubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein retention in Golgi apparatus	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein retention in Golgi apparatus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in regulation of ER to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of response to osmotic stress	IPI Inferred from Physical Interaction more info	PubMed
involved_in ribophagy	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Ubp3-Bre5 deubiquitination complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	HDA more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: mRNA-binding ubiquitin-specific protease UBP3

NP_011078.3

EC 3.4.19.12

Ubiquitin-specific protease that cleaves Ub-protein fusions; interacts with cofactor Bre5p to regulate transport between ER and Golgi, deubiquitinating COPII and COPI proteins, Sec23p and Sec27p; mediates steady-state retention of Golgi membrane proteins with Bre5p; phosphorylation (S695) by Hog1p regulates transcriptional activation by osmostress; inhibits Ras/PKA signaling through Ira2p; inhibits silencing; role in ribophagy; protein abundance increases in response to DNA replication stress

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001137.3 Reference assembly

Range

469686..472424 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179041.3 → NP_011078.3 TPA: mRNA-binding ubiquitin-specific protease UBP3 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011078.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D3DM58, Q01477

UniProtKB/TrEMBL

A6ZRA8, B3LRR4

Conserved Domains (1) summary

pfam00443
Location:460 → 908

UCH; Ubiquitin carboxyl-terminal hydrolase