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Information on EC 2.1.1.221 - tRNA (guanine9-N1)-methyltransferase and Organism(s) Schizosaccharomyces pombe and UniProt Accession O14214
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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: Schizosaccharomyces pombe
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, sctrm10, trna (guanine-n(1)-)-methyltransferase, m1g9 methyltransferase, trna m1g9 methyltransferase, trna m1r9 methyltransferase, tktrm10, htrmt10a, 
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 tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
Trm10 is specific for G9 of tRNAGly
-
-
?
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 tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
Trm10 is specific for G9 of tRNAGly
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SDR5C1 protein
enzyme TrmT10C requires another protein, SDR5C1 (MRPP2), to execute its m1R9 (G9 and A9) MTase and additional RNase P activity
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0032
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
additional information
additional information
kinetic mechanism of Trm10, overview
-
additional information
additional information
-
kinetic mechanism of Trm10, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0027
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.66
guanine9 in tRNAGly
tRNA from Schizosaccharomyces pombe, recombinant enzyme, pH and temperature not specified in the publication
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
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
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
additional information
enzyme overall structure analysis, active site structure, overview
additional information
-
enzyme overall structure analysis, active site structure, overview
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 free or in complex with S-adenosyl-L-homocysteine, X-ray diffraction structure determination and analysis at 2.0-2.5 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K110E/R121E/R127E
site-directed mutagenesis, inactive mutant
K208A
site-directed mutagenesis, mutation of a nucleoside binding pocket residue, the mutant shows 28% reduced activity compared to the wild-type enzyme
N209A
site-directed mutagenesis, the mutant shows increased Km for tRNA compared to the wild-type
Q118A
site-directed mutagenesis, mutation of a nucleoside binding pocket residue, inactive mutant
T244A
site-directed mutagenesis, mutation of a nucleoside binding pocket residue, the mutant shows 65% reduced activity compared to the wild-type enzyme
V206A
site-directed mutagenesis, mutation of a nucleoside binding pocket residue, the mutant shows 81% reduced activity compared to the wild-type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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. Purification of the recombinant TrmT10C-SDR5C1 wild-type and mutant complexes by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of N-terminally His-tagged enzyme Trm10 in Escherichia coli strain BL21/Gold(DE3), selenomethionine-labeled spTrm10_74 (residues 74-281) is expressed in Escherichia coli strain B834, recombinant wild-type and mutant Q226A TrmT10C (residues 40-403) is coexpressed with His-tagged protein SDR5C1
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
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)
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Release 2023.1 (January 2023)
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