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Information on EC 2.1.1.203 - tRNA (cytosine34-C5)-methyltransferase and Organism(s) Homo sapiens and UniProt Accession Q08J23

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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 .
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This record set is specific for:
Homo sapiens
UNIPROT: Q08J23
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Eukaryota, Archaea
Reaction Schemes
Synonyms
nsun3, nop2/sun domain family member 2, htrm4, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5-methylcytosine RNA methyltransferase
-
M5C RNA methyltransferase
-
NOP2/Sun domain family member 2
-
-
NSUN3 methylase
-
SAKI
-
-
substrate of AIM-1/Aurora kinase B
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
the formation of 5-methylcytosine34 is a strictly intron-dependent process
PATHWAY SOURCE
PATHWAYS
-
-
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].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA)
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
S-adenosyl-L-methionine + cytosine34 in tRNALeu(CAG) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu(CAG) precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytidine34 in mitochondrial tRNA
S-adenosyl-L-homocysteine + 5-methylcytidine34 in mitochondrial tRNA
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
show the reaction diagram
S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + microRNA 125b
S-adenosyl-L-homocysteine + ?
show the reaction diagram
-
the tRNA methyltransferase NSun2 methylates primary (pri-miR-125b), precursor (pre-miR-125b), and mature microRNA 125b (miR-125b) in vitro and in vivo
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
specific modification of cytosine34 in the intron-containing yeast pre-tRNALeu(CAA)
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNALeu(CAG) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu(CAG) precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytidine34 in mitochondrial tRNA
S-adenosyl-L-homocysteine + 5-methylcytidine34 in mitochondrial tRNA
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in mitochondrial tRNAMet(AUA) precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in mitochondrial tRNAMet(AUA) precursor
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + microRNA 125b
S-adenosyl-L-homocysteine + ?
show the reaction diagram
-
the tRNA methyltransferase NSun2 methylates primary (pri-miR-125b), precursor (pre-miR-125b), and mature microRNA 125b (miR-125b) in vitro and in vivo
-
-
?
additional information
?
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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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-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
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S-adenosyl-L-methionine
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
required
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
assay at
7.5
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
assay at
37
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
NSUN2 localizes to the nucleolus of Purkinje cells in the cerebellum
Manually annotated by BRENDA team
additional information
-
simultaneous overexpression of NSUN2 and METTL1, EC 2.1.1.33, is widely observed among human cancers
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
two of the seven NSUN proteins (NSUN3 and NSUN4) are synthesized on cytoplasmic ribosomes but localize to mitochondria
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
physiological function
evolution
-
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
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
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NSUN2_HUMAN
767
0
86471
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
86471
x * 86471, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 86471, calculated from sequence
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
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NSUN2 is phosphorylated at Ser139 by Aurora-B to inhibit its enzymatic activity during mitosis
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K190M
site-directed mutagenesis, catalytically inactive mutant
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
-
site-directed mutaegensis, the mutation to arginine at this residue causes NSUN2 to fail to localize within the nucleolus
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged NSun2 from Escherichia coli by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of the human Trm4 (hTrm4) cDNA in yeast partially complements the lack of the endogenous Trm4p enzyme
expression of wild-type and mutant enzymes in HCC1954 cells and in COS7 cells
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recombinant expression of His-tagged NSun2 in Escherichia coli
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transient expression of C-terminally Flag-tagged NSUN3 in HeLa cells, immunohistochemic analysis shows that NSUN3 predominantly localized in mitochondria
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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team