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Information on EC 2.1.1.221 - tRNA (guanine9-N1)-methyltransferase and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q12400
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2.1.1.221 tRNA (guanine9-N1)-methyltransferaseIUBMB Comments
The enzyme from Saccharomyces cerevisiae specifically methylates guanine9 [1,2]. The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of adenine9 in tRNA (cf. EC 2.1.1.218, tRNA (adenine9-N1)-methyltransferase) .
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Word Map
- 2.1.1.221
- microcephaly
- archaea
- disability
-
intellectual
- purine
-
stature
- eukarya
-
n1-methylation
-
monogenic
- puberty
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
+
guanine9 in tRNA
=
+
N1-methylguanine9 in tRNA
Synonyms
trm10, trmt10a, trmt10c, trna (guanine-n(1)-)-methyltransferase, m1g9 methyltransferase, trna m1g9 methyltransferase, trna m1r9 methyltransferase, tktrm10, htrmt10a, sctrm10, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + guanine9 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
catalytic mechanism and recognition of tRNA substrate, overview. The N-terminal extension of Trm10 is necessary for substrate tRNA recognition
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (guanine9-N1)-methyltransferase
The enzyme from Saccharomyces cerevisiae specifically methylates guanine9 [1,2]. The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of adenine9 in tRNA (cf. EC 2.1.1.218, tRNA (adenine9-N1)-methyltransferase) [1].
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 + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
S-adenosyl-L-methionine + guanine9 in tRNACysGCA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNACysGCA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
S-adenosyl-L-methionine + guanine9 in tRNAGlyCCC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGlyCCC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGlyGCC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGlyGCC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALeuCAA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALeuCAA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALeuGAG
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALeuGAG
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALysCUU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALysCUU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAPhe(G9)
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAPhe(G9)
tRNA from Saccharomyces cerevisiae
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAThrAGU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAThrAGU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAThrCGU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAThrCGU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAValUAC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAValUAC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
TRM10 is required for the catalysis of at least 9 of the 10 m1G modifications observed (tRNA(Trp), tRNA(Pro), tRNA(Val), tRNAi(Met), tRNA(Ile), tRNAICG(Arg), and both tRNAUCU(Arg) species) at position 9 in yeast. It is likely that Trm10p is also responsible for modification of G9 of tRNAAla
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
the enzyme is specific for guanine9 in tRNA, does not catalyse methylation of adenine9 in tRNA
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
Trm10 is specific for G9 of tRNAGly
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
tRNA from Saccharomyces cerevisiae
-
-
?
additional information
?
-
there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity, substrate specificity analysis in vivo, overview
-
-
?
additional information
?
-
-
there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity, substrate specificity analysis in vivo, overview
-
-
?
additional information
?
-
no activity of the enzyme with three sptRNAGly mutants at Position 9 (G9A, G9C, and G9U)
-
-
?
additional information
?
-
-
no activity of the enzyme with three sptRNAGly mutants at Position 9 (G9A, G9C, and G9U)
-
-
?
additional information
?
-
the yeast Trm10 enzyme does not exhibit activity on adenine9 residues in tRNA, no activity of EC 2.1.1.218
-
-
-
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 + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
S-adenosyl-L-methionine + guanine9 in tRNACysGCA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNACysGCA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
Trm10 is specific for G9 of tRNAGly
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGlyCCC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGlyCCC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGlyGCC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGlyGCC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALeuCAA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALeuCAA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALeuGAG
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALeuGAG
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNALysCUU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNALysCUU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAThrAGU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAThrAGU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAThrCGU
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAThrCGU
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAValUAC
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAValUAC
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
TRM10 is required for the catalysis of at least 9 of the 10 m1G modifications observed (tRNA(Trp), tRNA(Pro), tRNA(Val), tRNAi(Met), tRNA(Ile), tRNAICG(Arg), and both tRNAUCU(Arg) species) at position 9 in yeast. It is likely that Trm10p is also responsible for modification of G9 of tRNAAla
-
-
?
additional information
?
-
there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity, substrate specificity analysis in vivo, overview
-
-
?
additional information
?
-
-
there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity, substrate specificity analysis in vivo, overview
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
additional information
Trm10 does not depend on a catalytic metal ion
additional information
-
Trm10 does not depend on a catalytic metal ion
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0053
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
0.0024
guanine9 in tRNAGlyGCC
pH 8.0, 30°C, recombinant enzyme
-
0.00186
guanine9 in tRNAValUAC
pH 8.0, 30°C, recombinant enzyme
-
additional information
additional information
steady-state kinetics, overview
-
additional information
additional information
-
steady-state kinetics, overview
-
additional information
additional information
kinetic mechanism of Trm10, overview
-
additional information
additional information
-
kinetic mechanism of Trm10, overview
-
additional information
additional information
kinetic analysis of wild-type and mutant Trm10s, overview
-
additional information
additional information
-
kinetic analysis of wild-type and mutant Trm10s, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0028
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
0.009
guanine9 in tRNAGlyGCC
pH 8.0, 30°C, recombinant enzyme
-
0.0052
guanine9 in tRNAValUAC
pH 8.0, 30°C, recombinant enzyme
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.538
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
3.75
guanine9 in tRNAGlyGCC
pH 8.0, 30°C, recombinant enzyme
-
2.8
guanine9 in tRNAValUAC
pH 8.0, 30°C, recombinant enzyme
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
guanine9 methylation activity is not detectable in trm10-DELTA/trm10-DELTA strain
metabolism
the methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs. In some cases, these modifications have been shown to increase tRNA structural stability and induce correct tRNA folding. The m1A9 MTases belong to the Trm10 subfamily of the SPOUT superfamily. In addition to the m1A9 modification, the Trm10 subfamily of MTases methylates guanosine in some organisms
additional information
evolution
N-1 methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. The tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m1G9 modification in yeast
evolution
the enzyme Trm10 belongs to the SPOUT superfamily. Trm10 behaves as a monomer in solution, whereas other members of the SPOUT superfamily all function as homodimers. The MTase domain (the catalytic domain) of the Trm10 family displays a typical SpoU-TrmD (SPOUT) fold. Trm10 from Schizosaccharomyces pombe demonstrates identical tRNA MTase activity as Trm10 from Saccharomyces cerevisiae
evolution
aside from an active site aspartate residue, alignment of the available Trm10 protein structures and their primary sequences show no other obvious amino acid candidates in the active site that could account for the differences between m1G9-specific (Saccharomyces cerevisiae and Schizosaccharomyces pombe), m1A9-specific (Sulfolobus acidocaldarius) and m1A9/m1G9 dual-specific (human Trmt10C and Trm10 from Thermococcus kodakarensis) Trm10 MTases. It is possible that the purine specificity might simply be due to differences in surface charge around the active site and size and/or layout of the purine-binding pocket, which could allow different Trm10 family members to accommodate different purine substrates, rather than to specific residues for catalysis. The active site pocket is more open for the m1G9-specific Trmt10A and m1A9-specific Trm10, compared to the other Trm10 proteins. No obvious similarities are observed within the m1G9-specific group of proteins that are also clearly different from the m1A9-specific Trm10, and altered in the m1G9/m1A9 dual-specific protein
evolution
tRNA m1G9 methyltransferase (Trm10) is a member of the SpoU-TrmD (SPOUT) superfamily of methyltransferases, and Trm10 homologs are widely conserved throughout eukarya and archaea. Despite possessing the trefoil knot characteristic of SPOUT enzymes, Trm10 does not share the same quaternary structure or key sequences with other members of the SPOUT family, suggesting a distinct mechanism of catalysis. Sequence comparison of human TRMT10A and yeast Trm10. Trm10 does not depend on a catalytic metal ion, further distinguishing it from the other known SPOUT m1G methyltransferase, TrmD
additional information
enzyme overall structure analysis, active site structure, overview
additional information
-
enzyme overall structure analysis, active site structure, overview
additional information
the proposed aspartate general base D210 is not critical for methylation activity, mechanism of m1G9 methylation by Trm10. The pH-rate analysis suggests that D210 and other conserved carboxylate-containing residues at the active site collaborate to establish an active site environment that promotes a single ionization that is required for catalysis. Active site residues structure-function analysis
additional information
-
the proposed aspartate general base D210 is not critical for methylation activity, mechanism of m1G9 methylation by Trm10. The pH-rate analysis suggests that D210 and other conserved carboxylate-containing residues at the active site collaborate to establish an active site environment that promotes a single ionization that is required for catalysis. Active site residues structure-function analysis
additional information
tRNA recognition by Trm10 enzymes, overview
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
the enzyme adopts a globular alpha/beta structure consisting of six-stranded beta-sheets sandwiched by alpha-helices at both sides, small angle X-ray scattering analysis
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme in complex with S-adenosyl-L-homocysteine, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D210A
site-directed mutagenesis, the mutant does not abolish the mutant enzyme's activity, but modestly decreases it
D210K
site-directed mutagenesis, the mutant does not abolish the mutant enzyme's activity, but modestly decreases it
D210N
N212A
site-directed mutagenesis, the mutant shows increased Km for tRNA compared to the wild-type
D210N
site-directed mutagenesis, the mutant does not abolish the mutant enzyme's activity, but modestly decreases it
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography and dialysis, to 75-90% purity
recombinant N-terminally His-tagged enzyme Trm10 from Escherichia coli strain BL21/Gold(DE3) by nickel affinity chromatography, gel filtration, and anion exchange chromatography, followed by dialysis
recombinant N-terminally His6-tagged enzyme from Escherichia coli by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Trm10, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli
gene trm10, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli
recombinant expression of N-terminally His-tagged enzyme Trm10 in Escherichia coli strain BL21/Gold(DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Jackman, J.E.; Montange, R.K.; Malik, H.S.; Phizicky, E.M.
Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9
RNA
9
574-585
2003
Saccharomyces cerevisiae (Q12400), Saccharomyces cerevisiae
Kempenaers, M.; Roovers, M.; Oudjama, Y.; Tkaczuk, K.L.; Bujnicki, J.M.; Droogmans, L.
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA
Nucleic Acids Res.
38
6533-6543
2010
Saccharomyces cerevisiae (Q12400), Thermococcus kodakarensis (Q5JD38)
Shao, Z.; Yan, W.; Peng, J.; Zuo, X.; Zou, Y.; Li, F.; Gong, D.; Ma, R.; Wu, J.; Shi, Y.; Zhang, Z.; Teng, M.; Li, X.; Gong, Q.
Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate
Nucleic Acids Res.
42
509-525
2014
Saccharomyces cerevisiae (Q12400), Saccharomyces cerevisiae, Schizosaccharomyces pombe (O14214), Schizosaccharomyces pombe, Schizosaccharomyces pombe 972 (O14214)
Swinehart, W.E.; Henderson, J.C.; Jackman, J.E.
Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10
RNA
19
1137-1146
2013
Homo sapiens (Q8TBZ6), Saccharomyces cerevisiae (Q12400), Saccharomyces cerevisiae
Oerum, S.; Degut, C.; Barraud, P.; Tisne, C.
m1A Post-transcriptional modification in tRNAs
Biomolecules
7
20
2017
Homo sapiens (Q7L0Y3), Homo sapiens (Q8TBZ6), Saccharomyces cerevisiae (Q12400), Saccharomyces cerevisiae ATCC 204508 (Q12400), Schizosaccharomyces pombe (O14214), Schizosaccharomyces pombe 972 (O14214), Schizosaccharomyces pombe ATCC 24843 (O14214), Thermococcus kodakarensis (Q5JD38), Thermococcus kodakarensis ATCC BAA-918 (Q5JD38), Thermococcus kodakarensis JCM 12380 (Q5JD38)
EXTERNAL LINKS (specific for EC-Number 2.1.1.221)
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