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Information on EC 2.1.1.218 - tRNA (adenine9-N1)-methyltransferase
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EC Tree
2.1.1.218 tRNA (adenine9-N1)-methyltransferaseIUBMB Comments
The enzyme from Sulfolobus acidocaldarius specifically methylates adenine9 in tRNA . The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of guanine9 in tRNA (cf. EC 2.1.1.221, tRNA (guanine9-N1)-methyltransferase).
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The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
+
adenine9 in tRNA
=
+
N1-methyladenine9 in tRNA
Synonyms
trmt10b, htrmt10b, adenosine-specific trm10, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
adenosine-specific Trm10
EC 2.1.1.36
-
-
formerly, part transferred
-
m1A9 MTase
SaTrm10
SPOUT MTase
TkTrm10
Trm10
additional information
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + adenine9 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
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-
-
-
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (adenine9-N1)-methyltransferase
The enzyme from Sulfolobus acidocaldarius specifically methylates adenine9 in tRNA [1]. The bifunctional enzyme from Thermococcus kodakaraensis also catalyses the methylation of guanine9 in tRNA (cf. EC 2.1.1.221, tRNA (guanine9-N1)-methyltransferase).
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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 + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
S-adenosyl-L-methionine + adenine9 in tRNAArg
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAAsp
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAAsp
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAiMet
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAiMet
S-adenosyl-L-methionine + adenine9 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAPhe
tRNA substrate from Saccharomyces cerevisiae
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAThr
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAThr
tRNA substrate from Thermococcus kodakarensis
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNATrp
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNATrp
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
all the T-armless tRNAs possess 1-methyladenosine at position 9. This modification is structurally and functionally important for tRNAs in Ascaris suum mitochondria
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
the Watson-Crick base-pair-disrupting methyl group N1-methyladenine9 is sufficient for cloverleaf folding of human mitochondrial tRNALys
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
the enzyme is specific for adenine9 in tRNA, does not catalyse the methylation of guanine9 in tRNA from Saccharomyces cerevisiae. No m1A is formed in a mutant of the tRNAMeti where position 9 is occupied by a guanosine (tRNAMeti A9G)
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
the bifunctional enzyme catalyzes both methylation of guanine9 and methylation of adenine9 in tRNA
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
formation of N1-methyladenosine9 in tRNAAla from Thermococcus kodakaraensis that contains an adenine at position 9. The enzyme forms approximately the same amount of m1A and m1G when the tRNA of the yeast strain Y16243 is used as substrate. Given that occurrence of A9 and G9 in this tRNA population is almost equal (about 50% each) this result indicates that the enzyme TK0422p does not show any preference for one of these two nucleosides. The ratio m1A/m1G formed from Escherichia coli tRNA is higher than that with tRNA from the yeast Y16243 strain. This is consistent with the fact that there are about two times more tRNAs with A9 than with G9 in Escherichia coli. The enzyme is active in a pH range 5.5-9.75. The intensity of m1A and m1G spots varies greatly as a function of the pH. At pH 5.5, m1A MTase activity of TK0422p is predominant over m1G. At pH 7 or higher, both m1A and m1G are detected, m1G intensity growing with increasing pH
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAiMet
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAiMet
docking model of tRNAiMet of Sulfolobus acidocaldarius onto SaTrm10-SAH
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAiMet
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAiMet
docking model of tRNAiMet of Sulfolobus acidocaldarius onto SaTrm10-SAH
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-
?
additional information
?
-
substrate specificity analysis and comparison of hTRMT10A and hTRMT10B enzymes, overview. Purified hTRMT10B lacks m1G9 methyltransferase activity with several tested Saccharomyces cerevisiae and human tRNA substrates. hTRMT10A and hTRMT10B catalyze methylation of different tRNA substrates. hTRMT10B displays only very weak m1G9 activity on two substrates, human tRNAArg and tRNATrp, with no detectible activity on any other G9-containing tRNA. hTRMT10B, and not hTRMT10A, is indeed capable of catalyzing m1A9 methylation on tRNAAsp in vitro, while hTRMT10B has the sole responsibility for generating the m1A9 modification. hTRMT10A displays higher in vitro catalytic rates than hTRMT10B
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-
-
additional information
?
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-
substrate specificity analysis and comparison of hTRMT10A and hTRMT10B enzymes, overview. Purified hTRMT10B lacks m1G9 methyltransferase activity with several tested Saccharomyces cerevisiae and human tRNA substrates. hTRMT10A and hTRMT10B catalyze methylation of different tRNA substrates. hTRMT10B displays only very weak m1G9 activity on two substrates, human tRNAArg and tRNATrp, with no detectible activity on any other G9-containing tRNA. hTRMT10B, and not hTRMT10A, is indeed capable of catalyzing m1A9 methylation on tRNAAsp in vitro, while hTRMT10B has the sole responsibility for generating the m1A9 modification. hTRMT10A displays higher in vitro catalytic rates than hTRMT10B
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-
additional information
?
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the human Trm10C enzyme is bifunctional and methylates adenine9 (EC 2.1.1.218) and guanine9 (EC 2.1.1.221) residues in tRNA
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-
-
additional information
?
-
model for substrate tRNA binding by SaTrm10, in silico tRNA-SaTrm10 docking, role of Asp184 and Asp220 in the catalytic mechanism of SaTrm10, tRNA binding mechanism, overview
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-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
model for substrate tRNA binding by SaTrm10, in silico tRNA-SaTrm10 docking, role of Asp184 and Asp220 in the catalytic mechanism of SaTrm10, tRNA binding mechanism, overview
-
-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
the archaeal Trm10 enzyme does not exhibit activity on guanine9 residues in tRNA, no activity of EC 2.1.1.221
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-
-
additional information
?
-
the Trm10 enzyme from Thermococcus kodakarensis is bifunctional and methylates adenine9 (EC 2.1.1.218) and guanine9 (EC 2.1.1.221) residues in tRNA
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-
-
additional information
?
-
usage of [alpha-32P]-labeled tRNA substrates. The enzyme shows activity with both guanine9 and adenine9 containing tRNAs for methylation on N1. Bifunctional enzymes (catalyzing both m1A9 and m1G9) share the same rate-determining step for methylation as the monofunctional enzyme, these enzymes would also exhibit a different pattern of pH dependence for the two methylation reactions because of the difference in N1 pKa between adenine versus guanine
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-
-
additional information
?
-
the Trm10 enzyme from Thermococcus kodakarensis is bifunctional and methylates adenine9 (EC 2.1.1.218) and guanine9 (EC 2.1.1.221) residues in tRNA
-
-
-
additional information
?
-
the Trm10 enzyme from Thermococcus kodakarensis is bifunctional and methylates adenine9 (EC 2.1.1.218) and guanine9 (EC 2.1.1.221) residues in tRNA
-
-
-
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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 + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
S-adenosyl-L-methionine + adenine9 in tRNAArg
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAAsp
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAAsp
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNATrp
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNATrp
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
all the T-armless tRNAs possess 1-methyladenosine at position 9. This modification is structurally and functionally important for tRNAs in Ascaris suum mitochondria
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
the Watson-Crick base-pair-disrupting methyl group N1-methyladenine9 is sufficient for cloverleaf folding of human mitochondrial tRNALys
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
the bifunctional enzyme catalyzes both methylation of guanine9 and methylation of adenine9 in tRNA
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
no activity is detected in the absence of metal
Mg2+
required, the two tRNAs from Saccharomyces cerevisiae requires a much higher Mg2+ concentration (6-10 mM in the assay) for maximal TkTrm10 activity compared to the two Thermococcus kodakarensis tRNAs, for which maximal activity is observed at about 1 mM Mg2+ or less. Similar trends are exhibited for both m1G9 and m1A9 reactions, indicating that the identity of the target purine does not affect the observed metal dependencies
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Carcinoma
[Comparative study of the tRNA-methylases of normal and tumor tissues. II. Positional specificity of renal and carcinoma RA methylases]
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
enzyme kinetic analysis and modeling
-
additional information
additional information
single-turnover kinetic analysis of the enzyme with representative tRNA substrates, tRNAArg, tRNATrp, and tRNAAsp
-
additional information
additional information
-
single-turnover kinetic analysis of the enzyme with representative tRNA substrates, tRNAArg, tRNATrp, and tRNAAsp
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0093
adenine9 in tRNAPhe
pH 8.0, 40°C, recombinant enzyme, tRNA substrate from Saccharomyces cerevisiae
-
0.002
adenine9 in tRNAThr
pH 8.0, 50°C, recombinant enzyme, tRNA substrate from Thermococcus kodakarensis
-
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 9.75
the bifunctional enzyme is active in a pH range 5.5-9.75. The intensity of m1A and m1G spots varies greatly as a function of the pH. At pH 5.5, m1A MTase activity of TK0422p is predominant over m1G. At pH 7 or higher, both m1A and m1G are detected, m1G intensity growing with increasing pH
additional information
pH-rate profiles for the two activities catalyzed by the bifunctional methyltransferase TkTrm10, cf. EC 2.1.1.221
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 50
assay at, with Saccharomyces cervisiae tRNA and Thermococcus kodakarensis tRNA, respectively
50
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
hTRMT10B exhibits a restricted selectivity unusual for the Trm10 enzyme family
additional information
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
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
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
the enzyme belongs to the tRNA m1R9 methyltransferase (Trm10) family, which is conserved throughout eukarya and archaea. Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B. hTRMT10A and hTRMT10B are not biochemically redundant. hTRMT10A is the de facto methyltransferase responsible for all m1G9 formation on cytosolic tRNA, and hTRMT10B has a much more limited and specific role in tRNA processing in humans
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
-
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
-
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
-
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
-
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
-
malfunction
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
malfunction
mutation of catalytic residue Asp206 abolishes m1A9 activity in the archaeal Trm10 protein
malfunction
-
mutation of catalytic residue Asp206 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp206 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
-
malfunction
-
mutation of catalytic residue Asp184 abolishes m1A9 activity in the archaeal Trm10 protein
-
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
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
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
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
-
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
-
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
-
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
-
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
-
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
-
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
in human Trmt10C, the catalytic aspartate residue, found in archaeal m1A9 MTases, is replaced by leucine that, due to its uncharged nature, is likely to act differently in catalysis than a charged aspartate residue. Another aspartate residue is located deep in the active site pocket of human Trmt10C (Asp293) and might be involved in catalysis, but seems unlikely to be the determinant for m1A9 activity, as this position is occupied by aspartate in the m1G9-specific Trm10 proteins from yeast, and is not conserved in m1A9 active Trm10 proteins from Sulfolobus acidocaldarius and Thermococcus kodakarensis. tRNA recognition by Trm10 enzymes, overview
additional information
purified hTRMT10B lacks m1G9 methyltransferase activity with several tested Saccharomyces cerevisiae and human tRNA substrates
additional information
-
purified hTRMT10B lacks m1G9 methyltransferase activity with several tested Saccharomyces cerevisiae and human tRNA substrates
additional information
residue G202 is important for catalytic activity regardless of the target purine of the tRNA species to be modified
additional information
tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue, structure-function analysis, overview. N1-adenosine methylation by SaTrm10 requires two catalytic aspartate residues
additional information
tRNA recognition by Trm10 enzymes, overview
additional information
tRNA recognition by Trm10 enzymes, overview
additional information
-
tRNA recognition by Trm10 enzymes, overview
-
additional information
-
residue G202 is important for catalytic activity regardless of the target purine of the tRNA species to be modified
-
additional information
-
tRNA recognition by Trm10 enzymes, overview
-
additional information
-
tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue, structure-function analysis, overview. N1-adenosine methylation by SaTrm10 requires two catalytic aspartate residues
-
additional information
-
tRNA recognition by Trm10 enzymes, overview
-
additional information
-
tRNA recognition by Trm10 enzymes, overview
-
additional information
-
tRNA recognition by Trm10 enzymes, overview
-
Show AA Sequence and Transmembrane Helices (664 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
monomer
1 * 33200, native enzyme, SDS-PAGE, 1 * 35300, recombinant His-tagged enzyme, SDS-PAGE
monomer
-
1 * 33200, native enzyme, SDS-PAGE, 1 * 35300, recombinant His-tagged enzyme, SDS-PAGE
-
additional information
monomeric, full length SaTrm10 SAH displays an overall (tRNA resembling) L-shape and can be divided in three regions: a central domain (residues 89-246) which adopts a typical SPOUT fold, an N-terminal domain (residues 1-79) and a C-terminal helical domain (residues 247-292). The N-terminal domain is formed by a curved beta-sheet and two alpha-helices which together resemble a horse shoe
additional information
-
monomeric, full length SaTrm10 SAH displays an overall (tRNA resembling) L-shape and can be divided in three regions: a central domain (residues 89-246) which adopts a typical SPOUT fold, an N-terminal domain (residues 1-79) and a C-terminal helical domain (residues 247-292). The N-terminal domain is formed by a curved beta-sheet and two alpha-helices which together resemble a horse shoe
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant truncated construct of SaTrm10, lacking the C-terminal domain, native and enriched in selenomethionine (SaTrm10 1-249 and SaTrm10 1-249 SAD, respectively), hanging drop vapour diffusion, for SaTrm10 1-249: mixing of 15 mg/ml protein solution with an equal volume of crystallisation buffer containing 8% ethylene glycol, 0.1 M HEPES, pH 7.5, and 10% PEG 8000, for SaTrm10 1-249 SAD: mixing of 15 mg/ml protein solution with an equal volume of crystallisation buffer containing 2% dioxane, 0.05 M bicine, pH 9.0, and 15% PEG 20000, for full-length enzyme: mixing of 8 mg/ml protein in the presence of 1 mM SAH with an equal volume of crystallisation buffer containing 0.4 M (NH4)2SO4, 0.1 M sodium acetate, pH 4.5, and 15-20% PEG2000MME, several months, 20°C, X-ray diffraction structure determination and analysis at 2.1-2.4 A resolution, molecular replacement and modelling
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
G231R
site-directed mutagenesis, the mutation abolishs methylation of tRNAAsp and tRNATrp, with some residual (though reduced) activity on tRNAArg
G231R/G232R
site-directed mutagenesis, the double mutant displays no methylation activity on any of the three substrates
D184N
site-directed mutagenesis, kinetics and structure comparison
D220N
site-directed mutagenesis, kinetics and structure comparison
K121E
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
K185E
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
K249E
site-directed mutagenesis, the mutant is almost inactive
K38E
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
K5E
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
K64E
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
K75E
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
K78E
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
R276E
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
R288E
site-directed mutagenesis, the mutant is almost inactive
R47E
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
R74E
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
D220N
-
site-directed mutagenesis, kinetics and structure comparison
-
K75E
-
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
-
K78E
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
-
R276E
-
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
-
R47E
-
site-directed mutagenesis, the mutant shows very highly reduced activity compared to wild-type
-
D104A
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
D104A/E115Q/D245A
site-directed mutagenesis, almost inactive mutant
D104N
site-directed mutagenesis, the mutant shows slightly reduced activity compared to wild-type
D104N/D206N/D245N
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
D104N/D206N/D245N/E115Q
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
D206A
site-directed mutagenesis, the enzyme activity is modestly reduced compared to wild-type
D206A/D245A
site-directed mutagenesis, the enzyme activity is abolished in the double mutant
D206N
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
D245A
site-directed mutagenesis, the enzyme activity is modestly reduced compared to wild-type
D245N
site-directed mutagenesis, the mutation has no significant effect on the A-preference for TktRNAAsp, but exhibits a modest, but shows about 4fold reduced G-preference activity compared to wild-type
E115Q
site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type
G202R
site-directed mutagenesis, the mutant is nearly inactive, nearly complete loss of both m1G9 and m1A9 activity
G242R
site-directed mutagenesis, the mutant shows unaltered activity
Q122A
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged full-length wild-type enzyme, truncated enzyme SaTrm10 1-249, and enzyme mutants from Escherichia coli strain Rosetta (DE3)pLysS by nickel affinity chromatography and gel filtration, recombinant nontagged wild-type enzyme by anion exchange and cation exchange chromatography, followed by gel filtration
recombinant N-terminally His6-tagged protein from Escherichia coli by nickel affinity chromatography and dialysis
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene TK0422, sequence comparisons, recombinant expression of N-terminally His6-tagged protein in Escherichia coli
recombinant expression of His-tagged full-length wild-type enzyme, of truncated enzyme SaTrm10 1-249, and of enzyme mutants in Escherichia coli strain Rosetta (DE3)pLysS, recombinant expression of nontagged wild-type enzyme
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Helm, M.; Gieg, R.; Florentz, C.
A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys
Biochemistry
38
13338-13346
1999
Homo sapiens
brenda
Sakurai, M.; Ohtsuki, T.; Watanabe, K.
Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm
Nucleic Acids Res.
33
1653-1661
2005
Ascaris suum
brenda
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
Sulfolobus acidocaldarius (Q4J894), Thermococcus kodakarensis (Q5JD38)
brenda
Oerum, S.; Degut, C.; Barraud, P.; Tisne, C.
m1A Post-transcriptional modification in tRNAs
Biomolecules
7
20
2017
Sulfolobus acidocaldarius (Q4J894), Thermococcus kodakarensis (Q5JD38), Homo sapiens (Q7L0Y3), Thermococcus kodakarensis JCM 12380 (Q5JD38), Sulfolobus acidocaldarius DSM 639 (Q4J894), Thermococcus kodakarensis ATCC BAA-918 (Q5JD38), Sulfolobus acidocaldarius ATCC 33909 (Q4J894), Sulfolobus acidocaldarius NBRC 15157 (Q4J894), Sulfolobus acidocaldarius NCIMB 11770 (Q4J894), Sulfolobus acidocaldarius JCM 8929 (Q4J894)
brenda
Krishnamohan, A.; Dodbele, S.; Jackman, J.
Insights into catalytic and tRNA recognition mechanism of the dual-specific tRNA methyltransferase from Thermococcus kodakarensis
Genes (Basel)
10
100
2019
Thermococcus kodakarensis (Q5JD38), Thermococcus kodakarensis ATCC BAA-918 (Q5JD38)
brenda
Van Laer, B.; Roovers, M.; Wauters, L.; Kasprzak, J.; Dyzma, M.; Deyaert, E.; Singh, R.; Feller, A.; Bujnicki, J.; Droogmans, L.; Versees, W.
Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue
Nucleic Acids Res.
44
940-953
2016
Sulfolobus acidocaldarius (Q4J894), Sulfolobus acidocaldarius ATCC 33909 (Q4J894)
brenda
Howell, N.; Jora, M.; Jepson, B.; Limbach, P.; Jackman, J.
Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B
RNA
25
1366-1376
2019
Homo sapiens (Q6PF06), Homo sapiens
brenda
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