Information on EC 2.1.1.202 - multisite-specific tRNA:(cytosine-C5)-methyltransferase

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The expected taxonomic range for this enzyme is: Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
2.1.1.202
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RECOMMENDED NAME
GeneOntology No.
multisite-specific tRNA:(cytosine-C5)-methyltransferase
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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
S-adenosyl-L-methionine + cytosine40 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
show the reaction diagram
S-adenosyl-L-methionine + cytosine48 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine49 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
tRNA methylation (yeast)
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (multisite-cytosine-C5)-methyltransferase
The enzyme from Saccharomyces cerevisiae is responsible for complete 5-methylcytosine methylations of yeast tRNA. The incidence of modification depends on the cytosine position in tRNA. At positions 34 and 40, 5-methylcytosine is found only in two yeast tRNAs (tRNALeu(CUA) and tRNAPhe(GAA), respectively), whereas most other elongator yeast tRNAs bear either 5-methylcytosine48 or 5-methylcytosine49, but never both in the same tRNA molecule [1]. The formation of 5-methylcytosine34 and 5-methylcytosine40 is a strictly intron-dependent process, whereas the formation of 5-methylcytosine48 and 5-methylcytosine49 is an intron-independent process [2,3].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
two putative TRM4/NSUN2 paralogues, TRM4A and TRM4B
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
gene MJ0026
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Manually annotated by BRENDA team
strain Pp1001
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
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
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 + cytosine34 in tRNALeu precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine40 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
show the reaction diagram
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA precursor
show the reaction diagram
S-adenosyl-L-methionine + cytosine40 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine48 in tRNAAsp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAAsp precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAHis
show the reaction diagram
S-adenosyl-L-methionine + cytosine48 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNALeuCAA
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine49 in tRNAasp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAAsp precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNALeuCAA
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAHis
show the reaction diagram
S-adenosyl-L-methionine + cytosine50 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNALeuCAA
show the reaction diagram
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
show the reaction diagram
S-adenosyl-L-methionine + cytosine34 in tRNALeu precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNALeu precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine40 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine40 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine48 in tRNAAsp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAAsp precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine48 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAHis
show the reaction diagram
S-adenosyl-L-methionine + cytosine48 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNALeuCAA
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytosine49 in tRNAasp precursor
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAAsp precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine49 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNALeuCAA
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAAspGTC
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAAspGTC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAGly precursor
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAGly precursor
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAGlyGCC
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAGlyGCC
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAHis
show the reaction diagram
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?
S-adenosyl-L-methionine + cytosine50 in tRNALeuCAA
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNALeuCAA
show the reaction diagram
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?
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
additional information
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the S-adenosyl-L-methionine analigue sinefungin is bound in a negatively charged pocket near helix alpha8, binding structure, detailed overview
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5-aza-2'-deoxycytidine
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the catalytic mechanism is disrupted by the suicide inhibitor
5-azacytidine
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the catalytic mechanism is disrupted by the suicide inhibitor
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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levels of tRNAHis m5C increase following several nutrient starvation treatments of the BY4741 strain, Trm4 protein levels do not increase during starvation conditions
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 6.5
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maximal formation of Trm4p-RNA complexes observed in the pH range of 5.5-6.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
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tRNAHis m5C levels are unusually responsive to yeast growth conditions
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
77879
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x * 77879, calculated from sequence
80200
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x * 80200, calculated from sequence, including Hi26- and thrombin cleavage sequences
82200
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x * 82200, SDS-PAGE, recombinant enzyme including Hi26- and thrombin cleavage sequences
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 77879, calculated from sequence; x * 80200, calculated from sequence, including Hi26- and thrombin cleavage sequences; x * 82200, SDS-PAGE, recombinant enzyme including Hi26- and thrombin cleavage sequences
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Trm4 free and in complex with sinefungin, hanging-drop vapor diffusion, 0.001 ml of protein solution containing 10.8 mg/ml protein with 0.001 ml of crystallization solution containing 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, and 6% v/v isopropanol for MJ0026 alone, and 20 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, 3 mM sinefungin, and 10 mM cytidine for Mj0026 with sinefungin, cryoprotectant 20% glycerol and 20% PEG 400, respectively, X-ray diffraction structure determination and analysis at 1.27 A and 2.3 A resolutions, respectively
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant MJ0026 from Escherichia coli strain BL21-CodonPlus(DE3)-RIL by heat treatment, anion exchange and hydroxyapatite chromatography, and dialysis
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recombinant Ybl024p is purified to apparent homogeneity by one-step affinity chromatography on Ni21-NTA-agarose column
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene MJ0026, expression in Escherichia coli strain BL21-CodonPlus(DE3)-RIL
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inserted in the expression vector pET28b, and the corresponding protein is hyperexpressed in Escherichia coli BL21(DE3)
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trm4a and trm4b, phylogenetic analysis
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
levels of tRNAHis m5C increase following several nutrient starvation treatments of the BY4741 strain, Trm4 protein levels do not increase during starvation conditions
sequenced cDNA libraries prepared from small RNA isolated from NSUN2+/- and NSUN2-/- human fibroblasts reveal that eight of the 43 ncRNAs are differentially regulated
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C271A
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site-directed mutagenesis, the mutant enzyme forms an irreversible covalent crosslink between itself and the methylated cytosine in its target RNA
C260A
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the mutant enzyme forms stable RNA-protein complexes in vitro. The complexes are formed due to faulty product release by the modified Trm4p enzyme and contain only natural ribonucleotides within the RNA
C260S
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the mutant enzyme forms stable RNA-protein complexes in vitro. The complexes are formed due to faulty product release by the modified Trm4p enzyme and contain only natural ribonucleotides within the RNA
C310A
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the mutant shows only a slightly lower affinity for RNA compared to wild-type Trm4p. The C310A mutant of Trm4p is unable to bind RNA covalently as well as to transfer the methyl group from SAM to the RNA substrate since no activity was detectable
C424A
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organism containing the C424A mutation is not viable
C478A
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organism containing the C478A mutation is viable
additional information