TRM13 tRNA:m4X modification enzyme [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: TRM13
Official Full Name: tRNA:m4X modification enzyme
Primary source: SGD:S000005485
Locus tag: YOL125W
See related: AllianceGenome:SGD:S000005485; FungiDB:YOL125W; VEuPathDB:YOL125W
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 tRNA 2'-O-methyltransferase activity. Involved in tRNA nucleoside ribose methylation. Located in cytoplasm and nucleus. Orthologous to human TRMT13 (tRNA methyltransferase 13 homolog). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See TRM13 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (83834..85264)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Trm13 is a strongly diverged member of the Rossmann-fold MTase (RFM) superfamily, and therefore is evolutionarily related to 2'-O-MTases such as Trm7 and fibrillarin.
Title: Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site.
ORF YOL125w (TRM13) is necessary and sufficient for 2'-O-methylation at position 4 of yeast tRNA.
Title: The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4.

Submit: New GeneRIF Correction

Pathways from PubChem

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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 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables tRNA 2'-O-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables tRNA 2'-O-methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables tRNA 2'-O-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables tRNA methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in tRNA methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA methylation	IEA Inferred from Electronic Annotation more info
involved_in tRNA methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA nucleoside ribose methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: tRNA:m4X modification enzyme

NP_014516.1

EC 2.1.1.225

2'-O-methyltransferase; responsible for modification of tRNA at position 4; C-terminal domain has similarity to Rossmann-fold (RFM) superfamily of RNA methyltransferases

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_001147.6 Reference assembly

Range

83834..85264

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183379.2 → NP_014516.1 TPA: tRNA:m4X modification enzyme [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014516.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W1U3, Q12383

UniProtKB/TrEMBL

A6ZN86, B3LIU1, C7GV02, C8ZHJ1, N1NYR0

Conserved Domains (3) summary

pfam05206
Location:179 → 474

TRM13; Methyltransferase TRM13

pfam05253
Location:73 → 96

zf-U11-48K; U11-48K-like CHHC zinc finger

pfam11722
Location:19 → 47

zf-TRM13_CCCH; CCCH zinc finger in TRM13 protein