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Information on EC 2.1.1.202 - multisite-specific tRNA:(cytosine-C5)-methyltransferase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P38205

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IUBMB Comments
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 . 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].
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Saccharomyces cerevisiae
UNIPROT: P38205
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Word Map
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Eukaryota, Archaea
Reaction Schemes
hide(3 overall reactions are displayed. Show all (4)>>)
Synonyms
trdmt1, nsun6, trm4p, cytosine-5 rna methyltransferase, trm4b, rna:m5c methyltransferase, phnsun6, nop2/sun rna methyltransferase 2, trm4a, m5c rna methyltransferase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
multisite-specific tRNA:m5C-methyltransferase
-
tRNA:m5C-methyltransferase
-
RNA:m5C methyltransferase
-
-
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
S-adenosyl-L-methionine + cytosine40 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
show the reaction diagram
the formation of 5-methylcytosine34 is a strictly intron-dependent process
S-adenosyl-L-methionine + cytosine48 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
the formation of 5-methylcytosine48 is an intron-independent process
S-adenosyl-L-methionine + cytosine49 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
the formation of 5-methylcytosine49 is an intron-independent process
PATHWAY SOURCE
PATHWAYS
-
-
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].
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
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
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
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA
show the reaction diagram
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
show the reaction diagram
mini-tRNAPhe (composed of the anticodon stem-loop extended by the intron) is used to test the formation of m5C40. The formation of m5C40 is strictly intron dependent
-
-
?
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
S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA
show the reaction diagram
-
cf. EC 2.1.1.203
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNA precursor
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
show the reaction diagram
-
the entire intron, or the total precursor tRNA structure, is required for efficient suppressor function of the resultant mature tRNA. The reduced suppressor phenotype is correlated with lack of a 5-methylcytosine modification of the anticodon wobble base
-
-
?
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-methylcytosine49 in tRNA precursor
show the reaction diagram
-
the enzymatic formation of m5C at position 40 in the anticodon stem is strictly dependent on the presence of the intron. Enzymatic formation of m5C40 is independent of the whole architecture of the tRNA molecule and takes place on a minisubstrate composed of the anticodon stem nd loop of yeast tRNAPhe prolonged by its natural 19 nt intron
-
-
?
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 tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAHis
show the reaction diagram
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
-
yeast tRNA(GAA)
-
-
?
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + cytosine50 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAHis
show the reaction diagram
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
show the reaction diagram
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
S-adenosyl-L-methionine + cytosine40 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA
show the reaction diagram
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
S-adenosyl-L-methionine + cytosine48 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
show the reaction diagram
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
S-adenosyl-L-methionine + cytosine49 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
show the reaction diagram
the enzyme is responsible for complete m5C methylation of yeast tRNA. The frequency of modification depends on the cytosine position in tRNA. At positions 34 and 40, m5C is found only in two yeast tRNAs (tRNALeu (CUA) and tRNAPhe (GAA), respectively), whereas most other elongator yeast tRNAs bear either m5C48 or m5C49, but never both in the same tRNA molecule
-
-
?
S-adenosyl-L-methionine + cytosine34 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA
show the reaction diagram
-
cf. EC 2.1.1.203
-
-
?
S-adenosyl-L-methionine + cytosine40 in tRNA
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA
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 + cytosine48 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNAHis
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 + cytosine50 in tRNAHis
S-adenosyl-L-homocysteine + 5-methylcytosine50 in tRNAHis
show the reaction diagram
-
-
-
-
?
additional information
?
-
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the enzyme Trm4 fabricate 5-methylcytosine (m5C) in RNA molecules utilizing a dual-cysteine catalytic mechanism
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
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-
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
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
disruption of the ORF YBL024w leads to the complete absence of m5C in total yeast tRNA. No tRNA:m5C-methyltransferase activity towards all potential m5C methylation sites is detected in the extract of the disrupted yeast strain. The protein product of a single gene is responsible for complete m5C methylation of yeast tRNA
physiological function
the enzyme is responsible for complete m5C methylation of yeast tRNA
malfunction
-
yeast strains depleted of tRNAHis guanylyltransferase accumulate uncharged tRNAHis lacking the G-1 residue and subsequently accumulate additional 5-methylcytidine (m5C) at residues C48 and C50 of tRNAHis, due to the activity of the m5Cmethyltransferase Trm4. The increase in tRNAHis m5C levels does not require loss of Thg1, loss of G-1 of tRNAHis, or cell death but is associated with growth arrest following different stress conditions. Substantially increased tRNAHis m5C levels occur after temperature-sensitive strains are grown at nonpermissive temperature, and after wild-type strains are grown to stationary phase, starved for required amino acids, or treated with rapamycin. More modest accumulations of m5C in tRNAHis occur after starvation for glucose and after starvation for uracil. In virtually all cases examined, the additional m5C on tRNAHis occurs while cells are fully viable, and the increase is neither due to the GCN4 pathway, nor to increased Trm4 levels, phenotypes, overview. The increased amount of m5C is specific to tRNAHis. tRNAVal(AAC), which also normally has unmodified C48 and C50 residues adjacent to m5C49, has only marginally increased levels of m5C 7 h after temperature shift in the fcp1-1ts mutant
metabolism
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
77879
x * 77879, calculated from sequence
80200
x * 80200, calculated from sequence, including Hi26- and thrombin cleavage sequences
82200
x * 82200, SDS-PAGE, recombinant enzyme including Hi26- and thrombin cleavage sequences
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C260A
-
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
-
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant Ybl024p is purified to apparent homogeneity by one-step affinity chromatography on Ni21-NTA-agarose column
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
inserted in the expression vector pET28b, and the corresponding protein is hyperexpressed in Escherichia coli BL21(DE3)
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
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Motorin, Y.; Grosjean, H.
Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme
RNA
5
1105-1118
1999
Saccharomyces cerevisiae (P38205), Saccharomyces cerevisiae
Manually annotated by BRENDA team
King, M.Y.; Redman, K.L.
RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine
Biochemistry
41
11218-11225
2002
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Redman, K.L.
Assembly of protein-RNA complexes using natural RNA and mutant forms of an RNA cytosine methyltransferase
Biomacromolecules
7
3321-3326
2006
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Strobel, M.C.; Abelson, J.
Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo
Mol. Cell. Biol.
6
2663-2673
1986
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Jiang, H.Q.; Motorin, Y.; Jin, Y.X.; Grosjean, H.
Pleiotropic effects of intron removal on base modification pattern of yeast tRNAPhe: an in vitro study
Nucleic Acids Res.
25
2694-2701
1997
Saccharomyces cerevisiae, Saccharomyces cerevisiae Pp1001
Manually annotated by BRENDA team
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
Saccharomyces cerevisiae (P38205), Saccharomyces cerevisiae
Manually annotated by BRENDA team
Walbott, H.; Husson, C.; Auxilien, S.; Golinelli-Pimpaneau, B.
Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase
RNA
13
967-973
2007
Saccharomyces cerevisiae
Manually annotated by BRENDA team
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
Saccharomyces cerevisiae
Manually annotated by BRENDA team
Preston, M.; DSilva, S.; Kon, Y.; Phizicky, E.
TRNAHis 5-methylcytidine levels increase in response to several growth arrest conditions in Saccharomyces cerevisiae
RNA
19
243-256
2013
Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4741
Manually annotated by BRENDA team