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Information on EC 2.1.1.203 - tRNA (cytosine34-C5)-methyltransferase
for references in articles please use BRENDA:EC2.1.1.203
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EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.203 tRNA (cytosine34-C5)-methyltransferase
IUBMB Comments
The human enzyme is specific for C5-methylation of cytosine34 in tRNA precursors. The intron in the human pre-tRNALeu(CAA) is indispensable for the C5-methylation of cytosine in the first position of the anticodon. It is not able to form 5-methylcytosine at positions 48 and 49 of human and yeast tRNA precursors .
The enzyme appears in viruses and cellular organisms
- 2.1.1.203
- 5-methylcytosine
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anticodon
- homocysteine
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wobble
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ualcan
- 5-formylcytosine
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biallelic
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omnibus
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shrinkage
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hyperhomocysteinemia
- encephalomyopathy
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nsun2-mediated
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epitranscriptome
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early-onset
- medicine
- pharmacology
Reaction Schemes
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cytosine34 in tRNA precursor
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5-methylcytosine34 in tRNA precursor
Synonyms
nsun3, nop2/sun domain family member 2, htrm4, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5-methylcytosine RNA methyltransferase
EC 2.1.1.29
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formerly, part transferred
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M5C RNA methyltransferase
NSUN2
NSUN3
PMT1
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
the formation of 5-methylcytosine34 is a strictly intron-dependent process
S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
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PATHWAY SOURCE
PATHWAYS
MetaCyc
tRNA methylation (yeast)
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (cytosine34-C5)-methyltransferase
The human enzyme is specific for C5-methylation of cytosine34 in tRNA precursors. The intron in the human pre-tRNALeu(CAA) is indispensable for the C5-methylation of cytosine in the first position of the anticodon. It is not able to form 5-methylcytosine at positions 48 and 49 of human and yeast tRNA precursors [1].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytidine34 in mitochondrial tRNA
S-adenosyl-L-homocysteine + 5-methylcytidine34 in mitochondrial tRNA
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA)
Products: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
S-adenosyl-L-methionine + cytosine34 in tRNALeu(CAG) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu(CAG) precursor
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S-adenosyl-L-methionine + cytosine34 in tRNAMet
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAMet
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNAMet(CAU)
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAMet(CAU)
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNAPro
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAPro
S-adenosyl-L-methionine + microRNA 125b
S-adenosyl-L-homocysteine + ?
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Substrates: the tRNA methyltransferase NSun2 methylates primary (pri-miR-125b), precursor (pre-miR-125b), and mature microRNA 125b (miR-125b) in vitro and in vivo
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
Substrates: -
Products: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
Substrates: secondary structure of human mt-tRNAMet with modifications f5C and pseudouridine. The anticodon pairs with AUG and AUA codons, overview
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA). The hTrm4 MTase has a much narrower specificity against the yeast substrates than its yeast orthologue. The human enzyme is not able to form 5-methylcytosine34 at positions 48 and 49 of human and yeast tRNA precursors. Intron in the human pre-tRNALeu(CAA) is indispensable for the C5-methylation of cytosine in the first position of the anticodon. The modification of C34 depends on the nucleotide sequence surrounding the position to be modified and on the structure of intron-containing prolongated anticodon stem
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
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Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
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Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNAPro
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAPro
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNAPro
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAPro
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNAPro
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNAPro
Substrates: -
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additional information
?
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Substrates: NSUN-4 also mediates methylation of positions C628 and C632, as well as C631 in 18S rRNA
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additional information
?
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Substrates: levels of m5C changes site-specifically and dynamically in response to oxidative stress. All individual m5C sites showing significantly different methylation levels in NSUN2-rescued cells after 2 or 4 hours of stress. Methylation levels within the same tRNA molecule are independent from each other
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additional information
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Substrates: NSUN2-methylated tRNA sites are located in the anticodon loop (C34) and the VL (C46, C47), number of m5C per tRNA in all tRNAs or tRNA leucine, mass spectrometry, overview
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additional information
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Substrates: the Nsun2 fabricate 5-methylcytosine (m5C) in RNA molecules utilizing a dual-cysteine catalytic mechanism
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additional information
?
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Substrates: the enzyme forms covalent complexes with previously methylated RNA requiring S-adenosyl-L-homocysteine, the removal of this metabolite results in the disassembly of preexisting complexes
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additional information
?
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Substrates: NSun2 catalyzes the formation of cytosine-5 methylation in several tRNAs in vivo in tissues, including skin, liver, and testis
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additional information
?
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Substrates: the presence of a stable anticodon stem is found to be essential for formation of m5C34 of mt-tRNAMet by NSUN3
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytidine34 in mitochondrial tRNA
S-adenosyl-L-homocysteine + 5-methylcytidine34 in mitochondrial tRNA
Substrates: -
Products: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
Substrates: -
Products: -
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S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA)
Products: -
Products: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
S-adenosyl-L-methionine + cytosine34 in tRNALeu(CAG) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu(CAG) precursor
Substrates: -
Products: -
Products: -
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S-adenosyl-L-methionine + microRNA 125b
S-adenosyl-L-homocysteine + ?
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Substrates: the tRNA methyltransferase NSun2 methylates primary (pri-miR-125b), precursor (pre-miR-125b), and mature microRNA 125b (miR-125b) in vitro and in vivo
Products: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
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Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Substrates: -
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S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
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Substrates: -
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additional information
?
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Substrates: levels of m5C changes site-specifically and dynamically in response to oxidative stress. All individual m5C sites showing significantly different methylation levels in NSUN2-rescued cells after 2 or 4 hours of stress. Methylation levels within the same tRNA molecule are independent from each other
Products: -
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additional information
?
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Substrates: the Nsun2 fabricate 5-methylcytosine (m5C) in RNA molecules utilizing a dual-cysteine catalytic mechanism
Products: -
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additional information
?
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Substrates: NSun2 catalyzes the formation of cytosine-5 methylation in several tRNAs in vivo in tissues, including skin, liver, and testis
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
queuine
the addition of queuine to the growth medium increases C38 methylation from 10 to 100%, while other cytosines remain unaffected
queuine
PMT1 is strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels are stimulated by growth of cells in queuine-containing medium, in vitro Pmt1 activity is enhanced on Q-containing RNA; and queuine-stimulated in vivo methylation is abrogated by the absence of the eukaryotic tRNA-guanine transglycosylase
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Arteriosclerosis
NSun2 Deficiency Protects Endothelium From Inflammation via mRNA Methylation of ICAM-1.
Mitochondrial Diseases
Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
Mitochondrial Encephalomyopathies
Correction to: Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
Mitochondrial Encephalomyopathies
Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
Seizures
Correction to: Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
Seizures
Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
NSUN-4 acts as a dual rRNA and tRNA methyltransferase
SwissProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
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simultaneous overexpression of NSUN2 and METTL1, EC 2.1.1.33, is widely observed among human cancers
brenda
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NSUN2 localizes to the nucleolus of Purkinje cells in the cerebellum
brenda
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NSUN2 localizes to the nucleolus of Purkinje cells in the cerebellum
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
no obvious mitochondrial-targeting sequence is present in the N-terminal region of NSUN3, immunohistochemic analysis shows that NSUN3 predominantly localized in mitochondria
brenda
NSUN3 has been shown to localize to the mitochondrial matrix, its mitochondrial import has not been determined
brenda
NSUN3 has been shown to localize to the mitochondrial matrix, its mitochondrial import has not been determined
brenda
additional information
two of the seven NSUN proteins (NSUN3 and NSUN4) are synthesized on cytoplasmic ribosomes but localize to mitochondria
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brenda
additional information
two of the seven NSUN proteins (NSUN3 and NSUN4) are synthesized on cytoplasmic ribosomes but localize to mitochondria
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brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
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nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay. The tRNA modifying enzymes, NSUN2 and METTL1, EC 2.1.1.33, are mammalian orthologues of yeast Trm4 and Trm8, which are required for protecting tRNA against tRNA decay
malfunction
metabolism
physiological function
additional information
malfunction
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in mice, a Nsun2 knockout, ablation of Nsun2 through the deletion of exon 8, leads to the gross small-size phenotype indicating weight loss with 30% reduction at 3 months old, and partial alopecia at about 10 months old, suggesting a role for NSUN2 in skin homeostasis. Nsun2-/- males are sterile. Heterozygous mice appear normal and have no visible phenotype
malfunction
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mutation G679R causes NSUN2 to fail to localize within the nucleolus. NSUN2, besides other RNA-methyltransferase-encoding genes, is involved in neurological disorders like intellectual disability, also called mental retardation, phenotypes, overview
malfunction
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combined knockdown of NSUN2 and METTL1, EC 2.1.1.33, in HeLa cells drastically potentiate sensitivity of cells to 5-fluorouracil, but does not affect cisplatin- and paclitaxel-induced cytotoxicity, synergistic effects of NSUN2 and METTL1 double knockdown, which causes rapid tRNA(ValAAC) degradation induced by destabilizing 5-fluorouracil
malfunction
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in the absence of NSun2, tRNAs lack specific cytosine-5 methylation modifications, which can cause reduced protein translation rates. In NSun2-depleted testes, genes encoding Ddx4, Miwi, and Tudor domain-containing (Tdr) proteins are repressed, indicating that RNA-processing and posttranscriptional pathways are impaired. Proteins of the RNA-processing machinery are reduced in NSun2-/- testes. Loss of NSun2 specifically blocks meiotic progression of germ cells into the pachytene stage, as spermatogonial and Sertoli cells are unaffected in knockout mice. Lack of NSun2 causes a block of progression of the first prophase of male meiosis at the zygotene-pachytene stage before the chromatoid bodies first appear in the cytoplasm at the late pachytene stage. Phenotype, detailed overview
malfunction
NSUN3-knockout cells show strong reduction in mitochondrial protein synthesis and reduced oxygen consumption, leading to deficient mitochondrial activity. Reconstitution of formation of 5-methylcytidine (m5C) at position 34 (m5C34) on mt-tRNAMet with recombinant NSUN3 in the presence of AdoMet. Two disease-associated point mutations in mt-tRNAMet that impair m5C34 formation by NSUN3, are determined, indicating that a lack of f5C34 has pathological consequences. Loss of NSUN3 causes mitochondrial dysfunction, phenotype, overview
malfunction
mutation in (cytosine-5) RNA methyltransferase NSun2, which targets mostly tRNAs, impacts the expression of mobile element-derived sequences and affects DNA repeat integrity in Drosophila melanogaster. Reduced tRNA stability in the RCMT mutant indicates that tRNA-dependent processes affect mobile element expression and DNA repeat stability. NSun2 function affects mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in both RCMT mutants indicates that tRNA-dependent processes affect mobile element expression and DNA repeat stability. NSun2 mutants show heat-shock-independent transposable element (TE) expression changes
malfunction
loss-of-function mutations in the human NSUN3 gene causes mitochondrial disorders. NSUN2-depleted cells show attenuated changes to protein synthesis rates. Protein synthesis rates of rescued NSUN2-/- cells (NSUN2) are comparable to NSUN2+/+ cells and slightly, but not significantly, reduced when the enzymatic dead version of NSUN2 K190M is expressed. Cell stress causes a strong but temporary reduction of protein synthesis, which is attenuated by loss of NSUN2. Stress induces a site-specific and dynamic loss of m5C. Mitochondrial activity is reduced and catabolic pathways enhanced in the absence of NSUN2
malfunction
mutation of the cysteine in motif IV in human NSUN3 to alanine or serine results in a stable covalent intermediate. Lack of NSUN3 (or ALKBH1) impairs mitochondrial translation, leading to decreased cell proliferation. Mutations in NSUN3 that lead to either aberrant splicing and frameshifting (p.Glu42Valfs*11) or the introduction of a premature stop codon (c.295C>T/p.Arg99*) have been detected in patients with a mitochondrial deficiency disorder characterized by developmental disability microcephaly, failure to thrive, recurrent increased lactate levels in plasma, muscular weakness, proximal accentuated, external ophthalmoplegia, and convergence nystagmus. Furthermore, mitochondrial disease-associated point mutations with the gene encoding mt-tRNAMet that lead to A37G and C39U substitutions have been shown to impede methylation of C34 by NSUN3. In both cases, lack of NSUN3-mediated modification impairs mitochondrial translation, leading to reduced mitochondrial function. Reduced mitochondrial translation affects the normal differentiation program
malfunction
mutation of the cysteine in motif IV in human NSUN3 to alanine or serine results in a stable covalent intermediate
malfunction
m5C methyltransferase NSUN2 deficiency could negatively regulate the expression of hepatitis B virus (HBV). NSUN2-mediated m5C modification promotes the stability of HBV RNA. The replication level of HBV after NSUN2 knockdown decreases, and the ability of the mutant virus to infect and replicate in wild-type HepG2-NTCP cells and primary human hepatocytess is substantially impaired
malfunction
mutation G679R is linked to intellectual disability, diminishes NSUN2-mediated tRNA m5C in human cell lines. Mutant shows reduced binding to tRNA. Expressing human G679R in a Drosophila melanogaster NSUN2 mutant leads to the most severe social behavioral deficits. Expressing a NSUN2 variant lacking an internal intrinsically disordered region results in less pronounced deficits
metabolism
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formation of a covalent complex between dual-cysteine RNA:m5C methyltransferases and methylated RNA provides a unique means by which metabolic factors can influence RNA. By controlling the degree of formation of the enzyme-RNA covalent complex, S-adenosyl-L-homocysteine and pH are likely to influence the extent of m5C formation and the rate of release of methylated RNA from RNA:m5C methyltransferases. Metabolite-induced covalent complexes could plausibly affect the processing and function of m5C-containing RNAs
metabolism
the nucleolus, where NSUN2 resides, can act as a stress sensor. Nucleophosmin (NPMI) is a marker for nucleolar stress, and a rapid, strong down-regulation of both NPMI and NSUN2 is observed upon arsenite treatment. Additional NSUN family members residing in the mitochondria (NSUN3, NSUN4) and cytoplasm (NSUN6) are similarly repressed in response to arsenite stress
metabolism
during the maturation of the cytoplasmic tRNALeu(CAA), an m5C34 modification is also installed by the multisite-specific NSUN2 (cf. EC 2.1.1.202)
metabolism
during the maturation of the cytoplasmic tRNALeu(CAA), an m5C34 modification is also installed by the multisite-specific NSUN2 (cf. EC 2.1.1.202)
physiological function
specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA)
physiological function
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NSUN2 encodes a methyltransferase that catalyzes the intron-dependent formation of 5-methylcytosine at C34 of tRNA-leu(CAA). It also functions in spindle assembly during mitosis as well as chromosome segregation
physiological function
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NSUN2 encodes a methyltransferase that catalyzes the intron-dependent formation of 5-methylcytosine at C34 of tRNA-leu(CAA). It also functions in spindle assembly during mitosis as well as chromosome segregation
physiological function
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NSUN2 (NOP2/Sun domain family, member 2) is a NOL1/NOP2/SUN domain-containing tRNA (cytosine-5-)-methyltransferase. Nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay. The tRNA modifying enzyme NSUN2 is a mammalian orthologues of yeast Trm4, which is required for protecting tRNA against tRNA decay. Enzyme NUSN2 is not a critical regulator of cancer cell growth
physiological function
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NSun2 catalyzes the formation of cytosine-5 methylation in several tRNAs in vivo in tissues, including skin, liver, and testis. Functionally, the cytosine-5 methylation posttranscriptional modification influences translation rates, as well as correct RNA folding and stability. The mouse enzyme NSun2 is a component of the chromatoid body, NSun2 is essential for germ cell differentiation in the mouse testis. Cytosine-5 tRNA methyltransferases are dispensable for the spermatogonium and early spermatocytes
physiological function
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methylation by NSun2 inhibits the processing of pri-miR- 125b2 into pre-miR-125b2, decreases the cleavage of pre-miR-125b2 into miR-125, and attenuates the recruitment of RISC by miR-125, thereby repressing the function of miR-125b in silencing gene expression
physiological function
in human mitochondria, the AUA codon encodes methionine via a mitochondrial transfer RNA for methionine (mt-tRNAMet) that contains 5-formylcytidine (f5C) at the first position of the anticodon (position 34). f5C34 is required for deciphering the AUA codon during protein synthesis. Biogenesis of f5C34 is initiated by S-adenosylmethionine (AdoMet)-dependent methylation catalyzed by NSUN3, a methyltransferase in mitochondria. NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNAMet. NSUN3 is essential for f5C34 formation
physiological function
NSun2 protein is a highly conserved (cytosine-5) methyltransferases that methylate specific tRNAs instead of genomic DNA. NSun2 function affects repeat elements in a heat shock-independent fashion. NSun2, is an RCMT targeting the majority of tRNAs
physiological function
mutations in two (cytosine-5) RNA methyltransferase NSun2 impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila melanogaster. NSun2 function affects mobile element expression and genome integrity in a heat shock-independent fashion. Reduced tRNA stability in mutants indicates that tRNA-dependent processes affected mobile element expression and DNA repeat stability
physiological function
cytosine-5 RNA methylation links protein synthesis to cell metabolism. NSUN2 functions in the cell cycle to adapt dynamic protein synthesis in response to stress. Cytosine-5 RNA methylation is a metabolic sensor of external stress. NSUN2 regulates cell cycle phases and global protein synthesis during the cellular stress response. Cell stress causes a strong but temporary reduction of protein synthesis, which is attenuated by loss of NSUN2. In response to stress, the percentage of NSUN2+/+ cells decreased in the G1/G0-phase but increased in the S-phase and G2/M-phase of the cell cycle. In contrast, the cell cycle progression of NSUN2-/- cells remained stable, indicating that NSUN2-/- cells fail to adapt the cell cycle phases to the stress stimulus. A tight regulation of global protein synthesis might be needed to avoid accumulation of proteins during cell cycle arrest and repair. Dynamic changes of site-specific m5C levels require NSUN2. Site-specific tRNA methylation determines tRNA-derived fragments (tRFs) biogenesis in response to oxidative stress
physiological function
NSUN3 is a mitochondrial tRNA m5C methyltransferase that specifically targets the wobble position (C34) of mt-tRNAMet. The wobble base modification(s) installed by NSUN3 and ALKBH1 likely serve to expand codon recognition by mt-tRNAMet, enabling it to fulfil these diverse functions. Mt-tRNAMet-C34 is almost fully modified in vivo, and, although bisulfite and reduced bisulfite sequencing analyses indicate the presence of some m5C at this position, the majority undergoes further oxidation by ALKBH1 to generate 5-formylcytosine (f5C), structures of modified nucleotides at position 34 and the modification pathway. 5-Formylcytosine (f5C) has a well-established role in expanding codon recognition by mt-tRNAMet during mitochondrial translation. Modification of mt-tRNAMet by NSUN3 occurs in the mitochondria
physiological function
NSUN3 is a mitochondrial tRNA m5C methyltransferase that specifically targets the wobble position (C34) of mt-tRNAMet. Mt-tRNAMet-C34 is almost fully modified in vivo, and, although bisulfite and reduced bisulfite sequencing analyses indicate the presence of some m5C at this position, the majority undergoes further oxidation by ALKBH1 to generate 5-formylcytosine (f5C), structures of modified nucleotides at position 34 and the modification pathway. 5-Formylcytosine (f5C) has a well-established role in expanding codon recognition by mt-tRNAMet during mitochondrial translation. Modification of mt-tRNAMet by NSUN3 occurs in the mitochondria
physiological function
silencing NSUN2 decreases the global m5C levels, suppresses proliferation, migration and invasion, and inhibits activation of PI3K-AKT signaling in A549 and SPAC-1 cells. Phosphoinositide-3-kinase regulatory subunit 2 is upregulated by NSUN2-mediated m5C methylation by enhancing its mRNA stabilization
physiological function
the expression level of FABP5 mRNA decreases significantly when NSUN2 is knocked down
physiological function
inhibition of NSUN2 reduces cell proliferation, migration, colony formation and tube formation abilities. NSUN2-mediated m5C modification induces metabolic reprogramming and cell cycle by promoting the mRNA stabilities of ME1, GLUT3 and CDK2. Knockdown of NSUN2 attenuates tumorigenesis and angiogenesis in vivo. RNA m5C reader ALYREF is involved in NSUN2-mediated m5C modification in Cr (VI)-induced carcinogenesis. EP300 induced NSUN2 upregulation through transcriptional activation
physiological function
antioxidant-promoting transcription factor NRF2 is a target of NSUN2. Depleting NSUN2 increases the sensitivity of non-small cell lung cancer cells to ferroptosis activators both in vitro and in vivo. NSUN2 upregulates the expression of NRF2 by enhancing the stability of NRF2 mRNA through the m5C modification
physiological function
depletion of NSUN3 induces an increase of around eightfold in unmodified cytosines at position C34 in oral squamous cell carcinoma cell lines. NSUN3 and ALKBH1 together synthesize f5C34 modification, f5C is absent in mitochondrial-tRNAMet in NSUN3-depleted cells. The morphology of mitochondria in NSUN3-deficient cells is more circular and the number of cristae per mitochondrion is decreased
additional information
-
four active-site residues critical for Nsun2-mediated tRNA methylation are also required for the formation of the denaturant-resistant complexes with m5C-containing RNA
additional information
catalytic mechanism of the enzyme, comparison of NSUN family enzymes, overview. The NSUN family enzymes use the cysteine located in amino acid motif VI for the nucleophilic attack on carbon 6 of the target cytosine in RNA. In all seven human NSUN variants, the catalytic cysteine is preceded by threonine. Hydrogen bonding with the backbone carbonyl of proline and the aspartate side chain in motif IV orients the base in the active site and assists bond formation by transient protonation of the endocyclic N3 of cytidine. The activated nucleobase then accepts a methyl group from the properly positioned SAM cofactor, resulting in the formation of a carbon-carbon bond and generation of S-adenosylhomocysteine (SAH). To complete the reaction, the covalently bound methylated RNA has to be released from the protein. This elimination is assisted by the cysteine located in motif IV of NSUN proteins. This cysteine is located next to the conserved proline and acts as a base to deprotonate the tetrahedral carbon and initiate the elimination reaction that restores the unsaturated m5C heterocycle
additional information
catalytic mechanism of the enzyme, comparison of NSUN family enzymes, overview. The NSUN family enzymes use the cysteine located in amino acid motif VI for the nucleophilic attack on carbon 6 of the target cytosine in RNA. In all seven human NSUN variants, the catalytic cysteine is preceded by threonine. Hydrogen bonding with the backbone carbonyl of proline and the aspartate side chain in motif IV orients the base in the active site and assists bond formation by transient protonation of the endocyclic N3 of cytidine. The activated nucleobase then accepts a methyl group from the properly positioned SAM cofactor, resulting in the formation of a carbon-carbon bond and generation of S-adenosylhomocysteine (SAH). To complete the reaction, the covalently bound methylated RNA has to be released from the protein. This elimination is assisted by the cysteine located in motif IV of NSUN proteins. This cysteine is located next to the conserved proline and acts as a base to deprotonate the tetrahedral carbon and initiate the elimination reaction that restores the unsaturated m5C heterocycle
Show AA Sequence and Transmembrane Helices (1931 entries)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphoprotein
-
NSUN2 is phosphorylated at Ser139 by Aurora-B to inhibit its enzymatic activity during mitosis
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A37G
naturally occurring mutation, mitochondrial disease-associated point mutations with the gene encoding mt-tRNAMet that lead to A37G substitution, impede methylation of C34 by NSUN3, lack of NSUN3-mediated modification impairs mitochondrial translation, leading to reduced mitochondrial function
C39U
naturally occurring mutation, mitochondrial disease-associated point mutations with the gene encoding mt-tRNAMet that lead to C39U substitution, impede methylation of C34 by NSUN3, lack of NSUN3-mediated modification impairs mitochondrial translation, leading to reduced mitochondrial function
G679R
K190M
additional information
G679R
-
site-directed mutaegensis, the mutation to arginine at this residue causes NSUN2 to fail to localize within the nucleolus
G679R
mutation is linked to intellectual disability, diminishes NSUN2-mediated tRNA m5C in human cell lines. Mutant shows reduced binding to tRNA
additional information
generation of an insertion mutation in Drosophila NSun2 (NSun2DELTA21.5), which is viable and fertile and loses RNA methylation at known tRNA substrates. RNAi-mediated knockdown of NSun2 in follicle cells. Functional Gypsy retroviral particles can be formed in NSun2 mutants. Specific eccDNAs accumulate in RCMT mutants. RCMT mutants display reduced tRNA stability and tRNA abundance
additional information
-
combined knockdown of NSUN2 and METTL1, EC 2.1.1.33, in HeLa cells
additional information
generation of NSUN3 knockout cells. When the knockout strain is rescued by plasmid-encoded NSUN3, f5C34 in mt-tRNAMet is partially restored
additional information
-
generation of NSUN3 knockout cells. When the knockout strain is rescued by plasmid-encoded NSUN3, f5C34 in mt-tRNAMet is partially restored
additional information
generation of enzyme depeleted NSUN2-/- cells. Rescue for loss of NSUN2 by reexpressing the wild-type or enzymatic dead protein. The number of m5C per tRNA in all tRNAs or tRNA leucine is quantified by mass spectrometry in NSUN2-/- cells reexpressing wild-type NSUN2, the catalytically inactive NSUN2 K190M mutant, or the empty vector control. Reexpression of NSUN2 significantly restores 525 methylation sites when compared to the empty vector control and 431 sites when compared to K190M-overexpressing cells
additional information
mutation of the cysteine in motif IV in human NSUN3 to alanine or serine results in a stable covalent intermediate. Mutations in NSUN3 that lead to either aberrant splicing and frameshifting (p.Glu42Valfs*11) or the introduction of a premature stop codon (c.295C>T/p.Arg99*) have been detected in patients with a mitochondrial deficiency disorder
additional information
an NSUN2 v ariant lacking an internal intrinsically disordered region can install about 80% of wild-type's m5C within the nucleoplasm
additional information
mutation of the cysteine in motif IV in human NSUN3 to alanine or serine results in a stable covalent intermediate
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged NSun2 from Escherichia coli by nickel affinity chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of the human Trm4 (hTrm4) cDNA in yeast partially complements the lack of the endogenous Trm4p enzyme
gene NSun2, recombinant expression of wild-type and mutant enzymes
transient expression of C-terminally Flag-tagged NSUN3 in HeLa cells, immunohistochemic analysis shows that NSUN3 predominantly localized in mitochondria
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of NSUN2 and at least three of its m5C RNA methyltransferase family members are repressed in response to oxidative stress. Rapid and strong downregulation of NSUN2 upon arsenite treatment
NSUN2 is highly expressed in lung adenocarcinoma samples. MYC-associated zinc finger protein positively regulates the transcription of NSUN2
NSUN2 is significantly upregulated in Cr(VI)-transformed cells and lung tissues of Cr(VI)-exposed mice
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
molecular biology
a CRISPR-Cas13d-based tool, named reengineered m5C modification system (RCMS), for targeted m5C methylation and demethylation in specific transcripts. A nuclear-localized dCasRx conjugated to either a methyltransferase, NSUN2/NSUN6 , or a demethylase, the catalytic domain of mouse Tet2 (ten-eleven translocation 2), enables the manipulation of methylation events at precise m5C sites. It is effective in modulating m5C levels within transfer RNAs
pharmacology
-
enzymes NSUN2 and METTL1 are implicated in 5-fluorouracil sensitivity in HeLa cells. Interfering with methylation of tRNAs might provide a promising rationale to improve 5-fluorouracil chemotherapy of cancer
medicine
this methyltransferase is a novel downstream Myctarget which mediates Myc-induced cell proliferation and growth. Therefore, the characterization of hTrm4 substrate specificity can be essential since this enzyme is a potential target for cancer therapies
medicine
NSUN2 is highly expressed and causes elevated m5C methylation in lung adenocarcinoma samples. MYC-associated zinc finger protein positively regulates the transcription of NSUN2 and is related to poor survival of lung adenocarcinoma patients
medicine
m5C methyltransferase NSUN2 deficiency could negatively regulate the expression of hepatitis B virus (HBV). NSUN2-mediated m5C modification promotes the stability of HBV RNA. The replication level of HBV after NSUN2 knockdown decreases, and the ability of the mutant virus to infect and replicate in wild-type HepG2-NTCP cells and primary human hepatocytess is substantially impaired
medicine
isoform NSUN2 is highly expressed in osteosarcoma tissues and cells. Higher expression of NSUN2 predicts poorer prognosis of osteosarcoma patients. Both knocking down the expression of FABP5 and adding fatty acid oxidation inhibitor could counterbalance the promoting effect of NSUN2 on the progression of osteosarcoma
medicine
NSUN2 is significantly upregulated in Cr(VI)-transformed cells and lung tissues of Cr(VI)-exposed mice. RNA m5C reader ALYREF is involved in NSUN2-mediated m5C modification in Cr (VI)-induced carcinogenesis
medicine
NSUN2 expression levels strongly correlate with tumor grade and size in non-small cell lung cancer. NRF2 mRNA has a higher m5C level when NSUN2 is overexpressed in NSCLC cells
medicine
CD36-dependent non-dividing, metastasis-initiating tumour cells require require the mitochondrial RNA modifications m5C and f5C for palmitate-induced invasion of tumour cells. The NSUN3-driven gene signature is prognostic for lymph node metastasis and for higher pathological stage in patients with head and neck cancer
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Brzezicha, B.; Schmidt, M.; Makalowska, I.; Jarmolowski, A.; Pienkowska, J.; Szweykowska-Kulinska, Z.
Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu(CAA)
Nucleic Acids Res.
34
6034-6043
2006
Homo sapiens (Q08J23), Homo sapiens
brenda
Khan, M.A.; Rafiq, M.A.; Noor, A.; Hussain, S.; Flores, J.V.; Rupp, V.; Vincent, A.K.; Malli, R.; Ali, G.; Khan, F.S.; Ishak, G.E.; Doherty, D.; Weksberg, R.; Ayub, M.; Windpassinger, C.; Ibrahim, S.; Frye, M.; Ansar, M.; Vincent, J.B.
Mutation in NSUN2, which encodes an RNA methyltransferase, causes autosomal-recessive intellectual disability
Am. J. Hum. Genet.
90
856-863
2012
Homo sapiens, Mus musculus
brenda
Hussain, S.; Tuorto, F.; Menon, S.; Blanco, S.; Cox, C.; Flores, J.V.; Watt, S.; Kudo, N.R.; Lyko, F.; Frye, M.
The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation
Mol. Cell. Biol.
33
1561-1570
2013
Mus musculus
brenda
Moon, H.J.; Redman, K.L.
Trm4 and Nsun2 RNA:m5C methyltransferases form metabolite-dependent, covalent adducts with previously methylated RNA
Biochemistry
53
7132-7144
2014
Mammalia
brenda
Yuan, S.; Tang, H.; Xing, J.; Fan, X.; Cai, X.; Li, Q.; Han, P.; Luo, Y.; Zhang, Z.; Jiang, B.; Dou, Y.; Gorospe, M.; Wang, W.
Methylation by NSun2 represses the levels and function of microRNA 125b
Mol. Cell. Biol.
34
3630-3641
2014
Homo sapiens
brenda
Mueller, M.; Hartmann, M.; Schuster, I.; Bender, S.; Thuering, K.L.; Helm, M.; Katze, J.R.; Nellen, W.; Lyko, F.; Ehrenhofer-Murray, A.E.
Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine
Nucleic Acids Res.
43
10952-10962
2015
Dictyostelium discoideum (Q54JH6), Schizosaccharomyces pombe (P40999), Schizosaccharomyces pombe 972 (P40999)
brenda
Okamoto, M.; Fujiwara, M.; Hori, M.; Okada, K.; Yazama, F.; Konishi, H.; Xiao, Y.; Qi, G.; Shimamoto, F.; Ota, T.; Temme, A.; Tatsuka, M.
tRNA modifying enzymes, NSUN2 and METTL1, determine sensitivity to 5-fluorouracil in HeLa cells
PLoS Genet.
10
e1004639
2014
Homo sapiens
brenda
Genenncher, B.; Durdevic, Z.; Hanna, K.; Zinkl, D.; Mobin, M.B.; Senturk, N.; Da Silva, B.; Legrand, C.; Carre, C.; Lyko, F.; Schaefer, M.
Mutations in cytosine-5 tRNA methyltransferases impact mobile element expression and genome stability at specific DNA repeats
Cell Rep.
22
1861-1874
2018
Drosophila melanogaster (Q9W4M9)
brenda
Bohnsack, K.; Hoebartner, C.; Bohnsack, M.
Eukaryotic 5-methylcytosine (M5C) RNA methyltransferases mechanisms, cellular functions, and links to disease
Genes (Basel)
10
102
2019
Homo sapiens (Q9H649), Saccharomyces cerevisiae (Q9H649)
brenda
Nakano, S.; Suzuki, T.; Kawarada, L.; Iwata, H.; Asano, K.; Suzuki, T.
NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNAMet
Nat. Chem. Biol.
12
546-551
2016
Homo sapiens (Q9H649), Homo sapiens
brenda
Gkatza, N.A.; Castro, C.; Harvey, R.F.; Heiss, M.; Popis, M.C.; Blanco, S.; Borneloev, S.; Sajini, A.A.; Gleeson, J.G.; Griffin, J.L.; West, J.A.; Kellner, S.; Willis, A.E.; Dietmann, S.; Frye, M.
Cytosine-5 RNA methylation links protein synthesis to cell metabolism
PLoS Biol.
17
e3000297
2019
Homo sapiens (Q08J23)
brenda
Yang, M.; Wei, R.; Zhang, S.; Hu, S.; Liang, X.; Yang, Z.; Zhang, C.; Zhang, Y.; Cai, L.; Xie, Y.
NSUN2 promotes osteosarcoma progression by enhancing the stability of FABP5 mRNA via m5C methylation
Cell Death Dis.
14
125
2023
Homo sapiens (Q08J23)
brenda
Navarro, I.C.; Tuorto, F.; Jordan, D.; Legrand, C.; Price, J.; Braukmann, F.; Hendrick, A.G.; Akay, A.; Kotter, A.; Helm, M.; Lyko, F.; Miska, E.A.
Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans
EMBO J.
40
e105496
2021
Caenorhabditis elegans (Q95XR2)
brenda
Zhang, R.K.; Li, Y.; Sun, F.L.; Zhou, Z.H.; Xie, Y.X.; Liu, W.J.; Wang, W.; Qiu, J.G.; Jiang, B.H.; Wang, L.
RNA methyltransferase NSUN2-mediated m5C methylation promotes Cr(VI)-induced malignant transformation and lung cancer by accelerating metabolism reprogramming
Environ. Int.
192
109055
2024
Mus musculus (Q1HFZ0)
brenda
Chen, Y.; Jiang, Z.; Zhang, C.; Zhang, L.; Chen, H.; Xiao, N.; Bai, L.; Liu, H.; Wan, J.
5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer
J. Biol. Chem.
300
106793
2024
Homo sapiens (Q08J23)
brenda
Du, X.; Cheng, C.; Yang, Y.; Fan, B.; Wang, P.; Xia, H.; Ni, X.; Liu, Q.; Lu, L.; Wei, L.
NSUN2 promotes lung adenocarcinoma progression through stabilizing PIK3R2 mRNA in an m5C-dependent manner
Mol. Carcinog.
63
962-976
2024
Homo sapiens (Q08J23)
brenda
Delaunay, S.; Pascual, G.; Feng, B.; Klann, K.; Behm, M.; Hotz-Wagenblatt, A.; Richter, K.; Zaoui, K.; Herpel, E.; Muench, C.; Dietmann, S.; Hess, J.; Benitah, S.A.; Frye, M.
Mitochondrial RNA modifications shape metabolic plasticity in metastasis
Nature
607
593-603
2022
Homo sapiens (Q9H649)
brenda
Zhang, T.; Zhao, F.; Li, J.; Sun, X.; Zhang, X.; Wang, H.; Fan, P.; Lai, L.; Li, Z.; Sui, T.
Programmable RNA 5-methylcytosine (m5C) modification of cellular RNAs by dCasRx conjugated methyltransferase and demethylase
Nucleic Acids Res.
52
2776-2791
2024
Homo sapiens (Q08J23)
brenda
Gonskikh, Y.; Tirrito, C.; Bommisetti, P.; Mendoza-Figueroa, M.S.; Stoute, J.; Kim, J.; Wang, Q.; Song, Y.; Liu, K.F.
Spatial regulation of NSUN2-mediated tRNA m5C installation in cognitive function
Nucleic Acids Res.
53
gkae1169
2024
Homo sapiens (Q08J23)
brenda
Feng, J.; Xu, T.; He, M.; Li, J.; Yao, P.; Ma, C.; Yang, S.; Xu, Z.; Yan, K.; Chen, X.; Wang, H.; Liu, J.; Zeng, C.; Xia, Y.; Yan, H.; Zhou, L.; Chen, Y.
NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication
PLoS Pathog.
19
e1011808
2023
Homo sapiens (Q08J23)
brenda
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