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Information on EC 2.1.1.204 - tRNA (cytosine38-C5)-methyltransferase and Organism(s) Homo sapiens and UniProt Accession O14717
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2.1.1.204 tRNA (cytosine38-C5)-methyltransferaseIUBMB Comments
The eukaryotic enzyme catalyses methylation of cytosine38 in the anti-codon loop of tRNAAsp(GTC), tRNAVal(AAC) and tRNAGly(GCC). Methylation by Dnmt2 protects tRNAs against stress-induced cleavage by ribonuclease .
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Word Map
- 2.1.1.204
- methyltransferases
- n6-methyladenosine
- 5-methylcytosine
- mtases
-
2'-o-methylation
-
epitranscriptomic
-
methyltransferase-like
-
2'-o-methyltransferase
-
piwi-interacting
- mettl16
-
spout
The taxonomic range for the selected organisms is: Homo sapiens
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
+
cytosine38 in tRNA
=
+
5-methylcytosine38 in tRNA
Synonyms
rna methyltransferase, ddnmt2, dna methyltransferase 2, dnmt2 methyltransferase, pombe methyltransferase 1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytosine38 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
the enzyme forms a covalent enzyme-substrate intermediate with its target
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (cytosine38-C5)-methyltransferase
The eukaryotic enzyme catalyses methylation of cytosine38 in the anti-codon loop of tRNAAsp(GTC), tRNAVal(AAC) and tRNAGly(GCC). Methylation by Dnmt2 protects tRNAs against stress-induced cleavage by ribonuclease [3].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
-
in vitro transcribed tRNAAsp is methylated by DNMT2, albeit at reduced efficiency. Human, mouse, and Dictyostelium tRNA all are substrates for human DNMT2. C79, E119, R160 and R162 are essential for the catalytic mechanism of DNMT2
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
S-adenosyl-L-methionine + cytosine38 in tRNAAsp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp precursor
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAGly precursor
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAVal precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAVal precursor
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
methylates tRNAAsp specifically at cytosine38 in the anticodon loop. Human DNMT2 protein restores methylation in vitro to tRNAAsp from Dnmt2-deficient strains of mouse, Arabidopsis thaliana, and Drosophila melanogaster in a manner that is dependent on preexisting patterns of modified nucleosides. Unmodified tRNAAsp produced by in vitro transcription is not a substrate for DNMT2, which suggests that methylation is guided to cytosine38 by other modifications. Mannosylqueuosine is likely to be involved, because it is unique to tRNAAsp. Analysis of tRNAAsp sequences show complete conservation of the anticodon loop in species whose genomes encode Dnmt2 homologs, but the tRNAAsp anticodon loops in Caenorhabditis elegans and Saccharomyces cerevisiae, which lack Dnmt2 homologs, have diverged
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-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
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-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
-
mapping of the tRNA binding site of DNMT2 by systematically mutating surface-exposed lysine and arginine residues to alanine and studying the tRNA methylation activity and binding of the corresponding variants. tRNA specificity determinants and tRNA binding pocket structure in the DNMT2, overview
-
-
?
additional information
?
-
DNMT2 is able to methylate the cytosine 38 in the anticodon loop of aspartic acid transfer RNA instead of transferring methyl groups to the cytosine residues in the genomic DNA
-
-
-
additional information
?
-
-
DNMT2 induces a conformational change in the tRNA of the DNMT2-tRNA complex
-
-
?
additional information
?
-
-
DNMT2 functions primarily, if not exclusively, as a cytosine 5-methylation RNA methyltransferase with three verified tRNA targets: tRNAAsp, tRNAGly and tRNAVal
-
-
?
additional information
?
-
-
the enzyme DNMT2 is responsible for methylation of cytosine 38 in the anticodon loop of aspartic acid transfer RNA instead of transferring methyl group to the cytosine residues of DNA
-
-
?
additional information
?
-
-
development and evaluation of 5-azacytidine-mediated RNA immunoprecipitation, a mechanism-based technique in nine steps that exploits the covalent bond formed between an RNA methyltransferase and the cytidine analogue 5-azacytidine to recover RNA targets by immunoprecipitation, overview. High frequency of C>G transversions at the cytosine residues targeted by the enzyme, allowing identification of the specific methylated cytosine(s) in target RNAs. tRNAGly(GCC) bears one DNMT2 target site (C38)
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp precursor
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAGly precursor
-
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAVal precursor
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAVal precursor
-
-
-
-
?
additional information
?
-
-
DNMT2 functions primarily, if not exclusively, as a cytosine 5-methylation RNA methyltransferase with three verified tRNA targets: tRNAAsp, tRNAGly and tRNAVal
-
-
?
additional information
?
-
-
the enzyme DNMT2 is responsible for methylation of cytosine 38 in the anticodon loop of aspartic acid transfer RNA instead of transferring methyl group to the cytosine residues of DNA
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5-aza-2'-deoxycytidine
-
the catalytic mechanism is disrupted by the suicide inhibitor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten kinetic model
-
additional information
additional information
-
Michaelis-Menten kinetic model
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
expression of DNMTs in spermatogenetic cells in humans, enzyme DNMT2 is not involved, in contrast to the other DNMTs, overview
additional information
-
Dnmt2 is consistently upregulated in hundreds of tumor samples
additional information
-
in humans, DNMT2 mRNA is not transcribed in either any follicular stages of primordial, primary and secondary or in the GV, MI, and MII oocytes at Day 0 or Day 1, except for presence of a limited expression of DNMT2 in the MII oocytes, developmental expression analysis of DNMT2, overview
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
human DNMT2 protein (hDNMT2) is primarily localized to the cytoplasm of transfected mouse 3T3 fibroblasts
additional information
-
the major function of the N-terminal domain is to determine subcellular localization of the enzyme
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the DNMTs encompass three different structural regions: N-terminal regulatory domain, C-terminal catalytic domain and a central linker region. The N-terminal regulatory domain is particularly implicated in determining subcellular localization of the DNMT and in allocating unmethylated DNA strands from hemi-methylated ones. The C-terminal catalytic domain consists of 10 different characteristic motifs, and six of them (I, IV, VI, VIII, IX and X) are evolutionally conserved among mammals. General structure of mammalian DNA methyltransferases (DNMTs), overview. DNMT2 shows structural and functional differences when compared with the other DNMTs, it does not include N-terminal domain, and therefore cannot contribute to de-novo or maintenance methylation process
metabolism
analysis of aminoacylation of C38-methylated and unmethylated tRNAAsp
physiological function
evolution
malfunction
-
the enzyme knockout causes disruption of RNA methyltransferase activity
physiological function
physiological function
Dnmt2 RNA methyltransferase catalyses the methylation of C38 in the anticodon loop of tRNA-Asp. Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences. Proteins containing poly-Asp sequences in the human proteome often have roles in transcriptional regulation and gene expression. Hence, the Dnmt2-mediated methylation of tRNA-Asp exhibits a post-transcriptional regulatory role by controlling the synthesis of a group of target proteins containing poly-Asp sequences. Cytosine-38 methylation of tRNAAsp increases the rate of its aminoacylation
physiological function
enzyme DNMT2 carries out methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA. It is not involved in spermatogenesis
evolution
-
DNMT2 methylates RNA by employing a DNA methyltransferase-like catalytic mechanism, which is clearly different from the mechanism of other RNA MTases. DNMT2 has changed its substrate specificity from DNA to RNA in the course of its evolution
evolution
-
DNMT2 exhibits different expression patterns in different mammalian species. General structure of mammalian DNMTs: the enzymes are composed of three main parts: N-terminal regulatory domain, central linker region, and C-terminal catalytic domain. The N-terminal regulatory domain includes the following subdomains: charge rich-region, proliferating cell nuclear antigen-binding, nuclear localization signal, cytosine-rich zinc finger DNA-binding, polybromo homology, and tetrapeptide chromatin binding. The C-terminal catalytic domain includes six conserved motifs: the motif I contains an AdoMet binding site, the motif IV binds to substrate cytosine at its active site, the motif VI involves glutamyl residues serving as a donor, the motif IX maintains stability of the substrate-binding site, and the motif X functions in formation of the AdoMet binding site. DNMT2 is structurally and functionally different from other DNMTs because it does not possess the N-terminal regulatory domain
evolution
-
the enzyme belongs to the DNMT2 family of cytosine 5-methylation-RNA methyltransferases utilizing only one cysteine in their catalytic pocket
evolution
-
the enzyme is a highly conserved cytosine-C5 methyltransferase that introduces the C38 methylation of tRNA-Asp in many species, including lower eukaryotes, plants, insects and humans
physiological function
-
The DNMT2 protein methylates C38 of tRNA-Asp and it has a role in cellular physiology and stress response and its expression levels are altered in cancer tissues
physiological function
-
though DNMT2 has a catalytic domain at its C-terminus, it cannot catalyze either de novo or maintenance methylation process due to the absence of the N-terminal domain that enables other DNMT enzymes to bind DNA sequences and other regulatory proteins. DNMT2 is responsible for methylation of cytosine 38 in the anticodon loop of aspartic acid transfer RNA instead of transferring methyl group to the cytosine residues of DNA
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). TRDMT_HUMAN
391
0
44597
Swiss-Prot
other Location (Reliability: 2)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C292A
-
about 3fold reduction in RNA binding affinity. Significant residual activity
C79A
D217H
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
D226Y
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
D255Y
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
E119A
E185K
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
E202Q
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
E317G
-
site-directed mutagenesi, the mutant shows activity similar to the wild-type enzyme
E63K
-
site-directed mutagenesis, the mutation causes a twofold increase in activity compared to the wild-type enzyme
G155S
-
site-directed mutagenesis, the mutation causes an over fourfold decrease in activity compared to the wild-type enzyme
K122A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
K168A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K196A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K241A
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme
K251A
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme
K254A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K271A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K295A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
K346A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K363A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
K367A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
K387A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
L257V
-
site-directed mutagenesis, the mutation causes an over fourfold decrease in activity compared to the wild-type enzyme
M72I
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
N264S
-
site-directed mutagenesi, the mutant shows activity similar to the wild-type enzyme
R160A
R162A
R240A
-
site-directed mutagenesis, the mutant shows only slightly reduced activity compared to the wild-type enzyme
R275A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R288A
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme
R289A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R369A
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to the wild-type enzyme
R371A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R84A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R95A
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
additional information
C79A
-
about 3fold reduction in RNA binding affinity. No detectable in vitro methylation activity
E119A
-
mutant binds stronger to RNA than wild-type. No detectable in vitro methylation activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3)
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recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli to over 90% purity, except for mutant R84A, which is about 75% pure
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
phylogenetic analysis, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli
-
recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Jurkowski, T.P.; Meusburger, M.; Phalke, S.; Helm, M.; Nellen, W.; Reuter, G.; Jeltsch, A.
Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism
RNA
14
1663-1670
2008
Drosophila melanogaster, Homo sapiens
Goll, M.G.; Kirpekar, F.; Maggert, K.A.; Yoder, J.A.; Hsieh, C.L.; Zhang, X.; Golic, K.G.; Jacobsen, S.E.; Bestor, T.H.
Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2
Science
311
395-398
2006
Homo sapiens (O14717), Homo sapiens
Jurkowski, T.P.; Shanmugam, R.; Helm, M.; Jeltsch, A.
Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase
Biochemistry
51
4438-4444
2012
Homo sapiens
Elhardt, W.; Shanmugam, R.; Jurkowski, T.P.; Jeltsch, A.
Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties
Biochimie
112
66-72
2015
Homo sapiens
Uysal, F.; Akkoyunlu, G.; Ozturk, S.
Dynamic expression of DNA methyltransferases (DNMTs) in oocytes and early embryos
Biochimie
116
103-113
2015
Bos taurus, Homo sapiens, Mus musculus (O55055)
Khoddami, V.; Cairns, B.R.
Identification of direct targets and modified bases of RNA cytosine methyltransferases
Nat. Biotechnol.
31
458-464
2013
Homo sapiens
Shanmugam, R.; Fierer, J.; Kaiser, S.; Helm, M.; Jurkowski, T.P.; Jeltsch, A.
Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences
Cell Discov.
1
15010
2015
Homo sapiens (O14717), Homo sapiens, Mus musculus (O55055), Mus musculus
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