NCL1 tRNA (cytosine-C5-)-methyltransferase [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: NCL1
Official Full Name: tRNA (cytosine-C5-)-methyltransferase
Primary source: SGD:S000000120
Locus tag: YBL024W
See related: AllianceGenome:SGD:S000000120; FungiDB:YBL024W; VEuPathDB:YBL024W
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: TRM4
Summary: Enables tRNA (cytidine-5-)-methyltransferase activity and tRNA binding activity. Involved in cellular response to hydrogen peroxide and tRNA wobble base cytosine methylation. Located in nucleus. Human ortholog(s) of this gene implicated in autosomal recessive intellectual developmental disorder 5. Orthologous to human NSUN2 (NOP2/Sun RNA methyltransferase 2). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See NCL1 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 1

Sequence:: Chromosome: II; NC_001134.8 (172534..174588)

Chromosome II - NC_001134.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001134.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results provide evidence for a role of NCL1 in regulating metabolic homeostasis through translational control.
Title: Ncl1-mediated metabolic rewiring critical during metabolic stress.
analysis of how the carboxyl-terminal extension of yeast tRNA m5C methyltransferase enhances the catalytic efficiency of the amino-terminal domain
Title: The carboxyl-terminal extension of yeast tRNA m5C methyltransferase enhances the catalytic efficiency of the amino-terminal domain.
Cys310 of motif VI in Trm4p is essential for nucleophilic catalysis.
Title: Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase.

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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 RNA binding	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables tRNA (cytidine-5-)-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA (cytidine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables tRNA (cytidine-5-)-methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables tRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables tRNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA methylation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IMP Inferred from Mutant Phenotype more info	PubMed
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 processing	IEA Inferred from Electronic Annotation more info
involved_in tRNA wobble base cytosine methylation	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	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
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: tRNA (cytosine-C5-)-methyltransferase

NP_009529.1

EC 2.1.1.202

S-adenosyl-L-methionine-dependent tRNA: m5C-methyltransferase; methylates cytosine to m5C at several positions in tRNAs and intron-containing pre-tRNAs; increases proportion of tRNALeu(CAA) with m5C at wobble position in response to hydrogen peroxide, causing selective translation of mRNA from genes enriched in TTG codon; loss of NCL1 confers hypersensitivity to oxidative stress; similar to Nop2p and human proliferation associated nucleolar protein p120

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_001134.8 Reference assembly

Range

172534..174588

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178264.1 → NP_009529.1 TPA: tRNA (cytosine-C5-)-methyltransferase [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_009529.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VPX6, P38205

UniProtKB/TrEMBL

B3LNG1, C8Z3X2, G2W8Y5, N1P7E7

Conserved Domains (1) summary

COG0144
Location:1 → 411

RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]