URM1 ubiquitin-related modifier URM1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: URM1
Official Full Name: ubiquitin-related modifier URM1
Primary source: SGD:S000001270
Locus tag: YIL008W
See related: AllianceGenome:SGD:S000001270; FungiDB:YIL008W; VEuPathDB:YIL008W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables protein tag activity. Involved in several processes, including invasive growth in response to glucose limitation; protein urmylation; and tRNA wobble position uridine thiolation. Located in cytoplasm. Orthologous to human URM1 (ubiquitin related modifier 1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See URM1 in Genome Data Viewer

Location:: chromosome: IX

Exon count:: 1

Sequence:: Chromosome: IX; NC_001141.2 (342536..342835)

Chromosome IX - NC_001141.2 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001141.2

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ubiquitin-Related Modifier 1 (URM-1) Modulates Cx43 in Breast Cancer Cell Lines.
Title: Ubiquitin-Related Modifier 1 (URM-1) Modulates Cx43 in Breast Cancer Cell Lines.
The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
Title: The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
Redox requirements for ubiquitin-like urmylation of Ahp1, a 2-Cys peroxiredoxin from yeast.
Title: Redox requirements for ubiquitin-like urmylation of Ahp1, a 2-Cys peroxiredoxin from yeast.
A critical thioester linkage between Urm1 and Uba4 residue Cys225.This linkage is indispensable for the Urm1 intramolecular transfer between the two domains of Uba4 and it is thus, essential for tRNA thiolation.
Title: The Uba4 domain interplay is mediated via a thioester that is critical for tRNA thiolation through Urm1 thiocarboxylation.
ubiquitin-like Urm1.Uba4 systems are conserved and exchangeable between human and yeast cells
Title: Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man.
observations suggest that Urm1 activation is more similar to that of a prokaryotic sulfur carrier protein than that of a ubiquitin-like protein
Title: Urm1 couples sulfur transfer to ubiquitin-like protein function in oxidative stress.
Urm1p, the most ancient UBL, acts as a sulphur carrier in the process of eukaryotic transfer RNA (tRNA) modification, providing a possible evolutionary link between Ubiquitin-like proteins and sulphur transfer
Title: Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA.
ubiquitin-like protein Urm1 and ubiquitin-activating enzyme-like protein Uba4, as well as Tuc1 and Tuc2, were strictly required for tRNA thio-modification
Title: Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems.
Urm1 forms a dimer either in solution or in the crystal packing. The dimeric form will block the mobile C-terminal Gly-Gly, which could provide an autoprotection of this active site.
Title: Crystal structure of the dimeric Urm1 from the yeast Saccharomyces cerevisiae.
Data describe the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae.
Title: Solution structure of Urm1 and its implications for the origin of protein modifiers.

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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 protein tag activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein tag activity	IDA Inferred from Direct Assay more info	PubMed
enables protein tag activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in cell budding	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to oxidative stress	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to oxidative stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in invasive growth in response to glucose limitation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in invasive growth in response to glucose limitation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein urmylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein urmylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein urmylation	IEA Inferred from Electronic Annotation more info
involved_in protein urmylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA processing	IEA Inferred from Electronic Annotation more info
involved_in tRNA thio-modification	IEA Inferred from Electronic Annotation more info
involved_in tRNA wobble position uridine thiolation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA wobble uridine modification	IEA Inferred from Electronic Annotation more info
involved_in tRNA wobble uridine modification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-related modifier URM1

NP_012258.3

Ubiquitin-like protein involved in thiolation of cytoplasmic tRNAs; receives sulfur from the E1-like enzyme Uba4p and transfers it to tRNA; functions as a protein tag involved in the urmylation of proteins involved in nutrient sensing and the oxidative stress response; regulates stress-dependent condensate formation, promoting phase separation of numerous proteins to promote stress resilience and survival; forms co-condensates with Uba4p resulting in increased target urmylation

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_001141.2 Reference assembly

Range

342536..342835

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179358.3 → NP_012258.3 TPA: ubiquitin-related modifier URM1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012258.3

Status: REVIEWED

UniProtKB/Swiss-Prot

A6ZVR0, B3LTL7, D6VVS2, P40554

UniProtKB/TrEMBL

C7GJH9, C8ZAP1, G2WGD8, N1P0P4

Conserved Domains (1) summary

pfam09138
Location:3 → 99

Urm1; Urm1 (Ubiquitin related modifier)