TOM1 E3 ubiquitin-protein ligase TOM1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: TOM1
Official Full Name: E3 ubiquitin-protein ligase TOM1
Primary source: SGD:S000002865
Locus tag: YDR457W
See related: AllianceGenome:SGD:S000002865; FungiDB:YDR457W; VEuPathDB:YDR457W
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 ubiquitin-protein transferase activity. Involved in several processes, including endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); protein ubiquitination; and ubiquitin-dependent protein catabolic process. Located in nucleolus. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Turner type. Orthologous to human HUWE1 (HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See TOM1 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (1369790..1379596)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Coimmunoprecipitation analysis confirmed that Tom1 and Spo12 interact. Overexpression of Spo12 is cytotoxic in the absence of Tom1. Notably, Spo12 is degraded in S phase even in the absence of Tom1 and Cdh1, suggesting that an additional E3 ligase(s) also mediates Spo12 degradation
Title: The HECT-type ubiquitin ligase Tom1 contributes to the turnover of Spo12, a component of the FEAR network, in G2/M phase.
Together, these data point to an important role for Tom1, Ubc4 and Ubc5 in normal physiology and prompt the authors to refer to this pathway as ERISQ, for excess ribosomal protein quality control.
Title: A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins.
Tom1 and the Dia2 control Cdc6 degradation in G1 phase.
Title: The Hect domain E3 ligase Tom1 and the F-box protein Dia2 control Cdc6 degradation in G1 phase.
Data demonstrated that excess histones associate with Rad53, and also identified Ubc4 and Ubc5, as well as Tom1 as enzymes involved in the ubiquitylation of excess histones.
Title: Histone levels are regulated by phosphorylation and ubiquitylation-dependent proteolysis.

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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 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 transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleocytoplasmic transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleus organization	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 rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell size	HMP more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	HDA more info	PubMed
located_in nucleolus	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: E3 ubiquitin-protein ligase TOM1

NP_010745.3

EC 2.3.2.26

E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones; interacts with Dia2p and is required for Dia2p degradation; required to target Cdc6p for ubiquitin-mediated destruction during G1 phase

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_001136.10 Reference assembly

Range

1369790..1379596

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180765.3 → NP_010745.3 TPA: E3 ubiquitin-protein ligase TOM1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010745.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VT81, Q03280, Q7LIK7

UniProtKB/TrEMBL

G2WBI7, N1P5N7

Conserved Domains (5) summary

COG5021
Location:2385 → 3268

HUL4; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]

pfam06012
Location:92 → 387

DUF908; Domain of Unknown Function (DUF908)

pfam06025
Location:448 → 683

DUF913; Domain of Unknown Function (DUF913)

pfam14377
Location:2328 → 2357

DUF4414; Domain of unknown function (DUF4414)

NF033845
Location:1879 → 2061

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB