LCMT2 leucine carboxyl methyltransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LCMT2provided by HGNC
Official Full Name: leucine carboxyl methyltransferase 2provided by HGNC
Primary source: HGNC:HGNC:17558
See related: Ensembl:ENSG00000168806 MIM:611246; AllianceGenome:HGNC:17558
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PPM2; TYW4
Summary: The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008]
Orthologs: mouse all
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Genomic context

Location:: 15q15.3

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (43323649..43330573, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (41130950..41137880, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (43615847..43622771, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Kr-pok interacted directly with the DNA binding and oligomerization domains of p53. This interaction was essential for Kr-pok to bind the distal promoter region of the CDKN1A gene, p21WAF1, and to inhibit p53-mediated transcriptional activation of CDKN1A.
Title: KR-POK interacts with p53 and represses its ability to activate transcription of p21WAF1/CDKN1A.
This paper reports crystal structures of a yeast homolog, TYW4.
Title: Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA methyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in tRNA methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA modification	TAS Traceable Author Statement more info
involved_in wybutosine biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tRNA wybutosine-synthesizing protein 4

Names: p21WAF1/CIP1 promoter-interacting protein; tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase; tRNA(Phe) (7-(3-amino-3-carboxypropyl)wyosine(37)-O)-methyltransferase; tRNA-Wybutosine-synthesizing protein 4; tRNA-yW synthesizing protein 4

NP_055608.2

EC 2.1.1.290

EC 2.3.1.231

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_014793.5 → NP_055608.2 tRNA wybutosine-synthesizing protein 4

See identical proteins and their annotated locations for NP_055608.2

Status: REVIEWED

Source sequence(s)

AC009852, BC015949

Consensus CDS

CCDS10094.1

UniProtKB/Swiss-Prot

O60294, Q4JFT6, Q96B55, Q9NR10

UniProtKB/TrEMBL

A8K972

Related

ENSP00000307214.5, ENST00000305641.7

Conserved Domains (2) summary

pfam13415
Location:493 → 540

Kelch_3; Galactose oxidase, central domain

cl17173
Location:28 → 197

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...