UBR1 E3 ubiquitin-protein ligase UBR1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: UBR1
Official Full Name: E3 ubiquitin-protein ligase UBR1
Primary source: SGD:S000003416
Locus tag: YGR184C
See related: AllianceGenome:SGD:S000003416; FungiDB:YGR184C; VEuPathDB:YGR184C
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: PTR1
Summary: Enables proteasome regulatory particle binding activity and ubiquitin-protein transferase activity. Involved in several processes, including proteasomal protein catabolic process; protein ubiquitination; and regulation of dipeptide transport. Located in cytoplasm. Part of UBR1-RAD6 ubiquitin ligase complex and proteasome regulatory particle, base subcomplex. Used to study neurodegenerative disease. Human ortholog(s) of this gene implicated in Johanson-Blizzard syndrome and cardiovascular system disease. Orthologous to several human genes including UBR2 (ubiquitin protein ligase E3 component n-recognin 2). [provided by Alliance of Genome Resources, Oct 2024]
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Genomic context

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See UBR1 in Genome Data Viewer

Location:: chromosome: VII

Exon count:: 1

Sequence:: Chromosome: VII; NC_001139.9 (859901..865753, complement)

Chromosome VII - NC_001139.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001139.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Structural insights into Ubr1-mediated N-degron polyubiquitination.
Title: Structural insights into Ubr1-mediated N-degron polyubiquitination.
Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control.
Title: Direct involvement of Hsp70 ATP hydrolysis in Ubr1-dependent quality control.
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase.
Title: Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase.
Altered substrate recognition by Ubr1 accelerates proteasomal degradation of misfolded as well as native proteins at the endoplasmic reticulum membrane and in the cytosol. We term this pathway stress-induced homeostatically regulated protein degradation (SHRED) and propose that it promotes physiological adaptation.
Title: SHRED Is a Regulatory Cascade that Reprograms Ubr1 Substrate Specificity for Enhanced Protein Quality Control during Stress.
In addition to the E3 ubiquitin ligase Ubr1, we identified the prefoldin chaperone subunit Gim3 as an important quality control factor. We found that Gim3 interacted with the Guk1 mutant allele and propose that prefoldin promotes the degradation of the unstable model substrate by maintaining the solubility of the misfolded protein
Title: Prefoldin Promotes Proteasomal Degradation of Cytosolic Proteins with Missense Mutations by Maintaining Substrate Solubility.
The major ubiquitin ligase targeting the superfluous Fas2 subunit to the proteasome is Ubr1. The ubiquitin-conjugating enzymes Ubc2 and Ubc4 assist the degradation process.
Title: Quality control of a cytoplasmic protein complex: chaperone motors and the ubiquitin-proteasome system govern the fate of orphan fatty acid synthase subunit Fas2 of yeast.
Ubr1 Is Present at the endoplasmic reticulum membrane of wild-type cells and becomes a ligase for ER-associated protein degradation of Ste6* under heat and ethanol stress.
Title: Previously unknown role for the ubiquitin ligase Ubr1 in endoplasmic reticulum-associated protein degradation.
Data show that ubiquitin-protein ligases Ubr1 and Ubr2 have opposing roles in Ste11DeltaNK444R-GFP aggregation.
Title: A network of ubiquitin ligases is important for the dynamics of misfolded protein aggregates in yeast.
Study shows that the RING-type Ubr1 E3 and the HECT-type Ufd4 E3 interact, both physically and functionally.
Title: The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases.
Data suggest that Ubr1 and Ubr2 represent E3 components of a novel quality control pathway for proteins synthesized on cytosolic ribosomes.
Title: Ubr1 and Ubr2 function in a quality control pathway for degradation of unfolded cytosolic proteins.

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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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables proteasome regulatory particle binding	IPI Inferred from Physical Interaction more info	PubMed
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-protein transferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in ERAD pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to unfolded protein	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to unfolded protein	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cytoplasm protein quality control by the ubiquitin-proteasome system	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cytoplasm protein quality control by the ubiquitin-proteasome system	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondria-associated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein monoubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of dipeptide transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosome-associated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stress-induced homeostatically regulated protein degradation pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of UBR1-RAD6 ubiquitin ligase complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IGI Inferred from Genetic Interaction more info	PubMed
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
part_of proteasome regulatory particle, base subcomplex	IPI Inferred from Physical Interaction more info	PubMed
part_of ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UBR1

NP_011700.1

EC 2.3.2.27

E3 Ub-ligase (N-recognin); recognizes and ubiquitinates N-end rule pathway substrates in complex with Rad6p; Roq1p-bound form accelerates degradation of misfolded and native ER membrane and cytosolic proteins as part of the stress-induced homeostatically regulated protein degradation (SHRED) pathway; role in ER-associated protein degradation; modifies Cup9p to regulate peptide transport; mutation in human UBR1 causes Johansson-Blizzard Syndrome (JBS)

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_001139.9 Reference assembly

Range

859901..865753 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181313.1 → NP_011700.1 TPA: E3 ubiquitin-protein ligase UBR1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011700.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VUW7, P19812

UniProtKB/TrEMBL

G2WER3, N1P9X8

Conserved Domains (5) summary

smart00396
Location:121 → 193

ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway

cd00162
Location:1286 → 1323

RING_Ubox; RING-H2 finger (C3H2C3-type) [structural motif]

pfam18995
Location:1402 → 1793

PRT6_C; Proteolysis_6 C-terminal

cl00933
Location:308 → 358

ClpS; ATP-dependent Clp protease adaptor protein ClpS

cl17238
Location:1286 → 1332

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain