RKR1 ubiquitin-protein ligase RKR1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RKR1
Official Full Name: ubiquitin-protein ligase RKR1
Primary source: SGD:S000004861
Locus tag: YMR247C
See related: AllianceGenome:SGD:S000004861; FungiDB:YMR247C; VEuPathDB:YMR247C
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: LTN1
Summary: Enables ribosomal large subunit binding activity and ubiquitin protein ligase activity. Involved in several processes, including rescue of stalled ribosome; ribosome-associated ubiquitin-dependent protein catabolic process; and subtelomeric heterochromatin formation. Located in nucleus. Part of RQC complex. Is active in cytosolic ribosome. Orthologous to human LTN1 (listerin E3 ubiquitin protein ligase 1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See RKR1 in Genome Data Viewer

Location:: chromosome: XIII

Exon count:: 1

Sequence:: Chromosome: XIII; NC_001145.3 (763351..768039, complement)

Chromosome XIII - NC_001145.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001145.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides.
Title: Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides.
Our findings suggest that carboxy-terminal alanine and threonine residues aggregation is detrimental, rather than adaptive, in cells with diminished Ltn1 function.
Title: Aggregation of CAT tails blocks their degradation and causes proteotoxicity in S. cerevisiae.
The authors determined that the Rqc2p-mediated Carboxy-terminal Alanine and Threonine (CAT) tail elongation is mechanistically distinct from canonical translation, that Ltn1p-mediated ubiquitination depends on the poorly characterized Ribosome-associated Quality control Complex (RQC) component Rqc1p, and that the process of CAT tailing enables robust ubiquitination of the nascent polypeptide.
Title: In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing.
Data show that Saccharomyces cerevisiae proteins Rqc1, Ltn1, and Cdc48 prevent the aggregation of aberrant proteins that can only appear after C-terminal alanine-threonine tail (CAT-tail) addition by Rqc2.
Title: Rqc1 and Ltn1 Prevent C-terminal Alanine-Threonine Tail (CAT-tail)-induced Protein Aggregation by Efficient Recruitment of Cdc48 on Stalled 60S Subunits.
findings can explain the proteotoxicity of ribosome-stalled polypeptides and demonstrate the essential role of the RQC in maintaining proteostasis
Title: Failure of RQC machinery causes protein aggregation and proteotoxic stress.
Our results indicate that Rkr1 plays the primary role in targeting the tested model ER-targeted nonstop and translationally stalled proteins for degradation
Title: Rkr1/Ltn1 Ubiquitin Ligase-mediated Degradation of Translationally Stalled Endoplasmic Reticulum Proteins.
Ltn1 and Ubp3-Bre5 likely contribute to adapt ribophagy activity to both nutrient supply and protein translation.
Title: Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy.
Data show that Ltn1 E3 ligase has an elongated form and presents a continuum of conformational states about two flexible hinge regions.
Title: Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase.
These results identify a new participant (Rkr1) in a protein ubiquitylation pathway within the nucleus that acts to modulate chromatin function and transcription.
Title: Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae.

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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 ribosomal large subunit binding	IBA Inferred from Biological aspect of Ancestor more info
enables ribosomal large subunit binding	IDA Inferred from Direct Assay 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	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay 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 chromatin organization	IGI Inferred from Genetic Interaction more info	PubMed
involved_in proteasomal protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in proteasomal protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rescue of stalled ribosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in rescue of stalled ribosome	IDA Inferred from Direct Assay more info	PubMed
involved_in rescue of stalled ribosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosome-associated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosome-associated ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ribosome-associated ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
involved_in ribosome-associated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in subtelomeric heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of RQC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RQC complex	IDA Inferred from Direct Assay more info	PubMed
part_of RQC complex	IEA Inferred from Electronic Annotation more info
part_of RQC complex	IPI Inferred from Physical Interaction more info	PubMed
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in cytosolic ribosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-protein ligase RKR1

NP_013975.1

EC 2.3.2.27

RING domain E3 ubiquitin (Ub) ligase; role in Ub-mediated degradation of non-stop proteins and translationally stalled ER membrane proteins; component of ribosome-bound RQC (ribosome quality control) complex; role in the turnover of stalled nascent chain polypeptides through lysine residues exposed by CAT (C-terminal alanine and threonine) tailing; degrades mRNA products lacking a termination codon; role in chromatin modification; mutations in mouse homolog Listerin elicit neurodegeneration