Information on EC 2.1.1.204 - tRNA (cytosine38-C5)-methyltransferase

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The expected taxonomic range for this enzyme is: Coelomata

EC NUMBER
COMMENTARY
2.1.1.204
-
RECOMMENDED NAME
GeneOntology No.
tRNA (cytosine38-C5)-methyltransferase
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
S-adenosyl-L-methionine + cytosine38 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
-
-
-
-
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].
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Dnmt2
-
gene name
DNMT2 methyltransferase
-
-
hDNMT2
O14717
gene name
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
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
malfunction
-
knockdown of Dnmt2 protein in zebrafish embryos confers differentiation defects in particular organs, including the retina, liver, and brain
malfunction
Q9U6H7
Drosophila Dnmt2 mutants show reduced viability under stress conditions, and Dnmt2 relocalizes to stress granules following heat shock
physiological function
-
Dnmt2 methylates an RNA species of about 80 bases, consistent with tRNA methylation. Thus, Dnmt2 promotes zebrafish development, likely through cytoplasmic RNA methylation
physiological function
Q9U6H7
RNA methylation by Dnmt2 protects tRNAs against stress-induced cleavage by ribonuclease
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
O14717
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
Q9U6H7
RNA methylation by Dnmt2 protects tRNAs against stress-induced cleavage
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
-
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 tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
O14717
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
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
Q9U6H7
methylation of cytosine 38 in the anti-codon lopp of tRNAAsp(GTC), tRNAVal(AAC) and tRNAGly(GCC). Other C38-containing tRNAs-including tRNAMet(ATG), tRNAGlu(CTC), and tRNAHis(GTG) are not detectably methylated in a Dnmt2-dependent manner
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
show the reaction diagram
-
-, 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 induces a conformational change in the tRNA of the DNMT2-tRNA complex
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-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
O14717
-
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
show the reaction diagram
Q9U6H7
RNA methylation by Dnmt2 protects tRNAs against stress-induced cleavage
-
-
?
S-adenosyl-L-methionine + cytosine38 in tRNAAsp
S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNAAsp
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
-
supports native folding of the substrate tRNA
Mg2+
-
required
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
8
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
-
ubiquitously expressed during early embryogenesis. Expression remains ubiquitous throughout development with enrichment in the foregut and hindgut as well as in the developing mesoderm in gastrulating embryos. Dnmt2 proteins are enriched in actively dividing cells. Dnmt2 localization is highly dynamic during the cell cycle
Manually annotated by BRENDA team
-
Dnmt2-EGFP is highly expressed in the germarium, blastocyst and cyst stages of the female germ line with the exception of follicle cells. Dnmt2-EGFP is mostly present in the cytoplasm but can also be found in nurse cell nuclei. In the male germ line, Dnmt2-EGFP is expressed in most cells, including stem cells as well as in maturing spermatocytes with the exception of the post-mitotic hub cells
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Q9U6H7
granular cytoplasmic distribution with minor signals in the nucleus. Large structures appear in the cytoplasm and in the nucleus upon heat stress
Manually annotated by BRENDA team
-
Dnmt2 is both a cytoplasmic and a nuclear protein
Manually annotated by BRENDA team
O14717
human DNMT2 protein (hDNMT2) is primarily localized to the cytoplasm of transfected mouse 3T3 fibroblasts
Manually annotated by BRENDA team
-
Dnmt2 is both a cytoplasmic and a nuclear protein. A significant amount of Dnmt2 is bound to the nuclear matrix. Dnmt2-EGFP(enhanced-green-fluorescent-protein) enters prophase nuclei and shows a spindle-like localization pattern during mitotic divisions. This localization is microtubule dependent. Dnmt2 can access DNA during mitotic cell divisions
Manually annotated by BRENDA team
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
structural modeling of DNMT2, overview
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli to over 90% purity, except for mutant R84A, which is about 75% pure
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
expression in NIH3T3 cells
O14717
phylogenetic analysis, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli
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ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C292A
-
about 3fold reduction in RNA binding affinity. Significant residual activity
C79A
-
about 3fold reduction in RNA binding affinity. No detectable in vitro methylation activity
C79A
-
site-directed mutagenesis, inactive mutant
E119A
-
mutant binds stronger to RNA than wild-type. No detectable in vitro methylation activity
E119A
-
site-directed mutagenesis, inactive mutant
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
R160A
-
no detectable in vitro methylation activity
R160A
-
site-directed mutagenesis, inactive mutant
R162A
-
no detectable in vitro methylation activity
R162A
-
site-directed mutagenesis, inactive mutant
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