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Information on EC 2.1.1.221 - tRNA (guanine9-N1)-methyltransferase and Organism(s) Thermococcus kodakarensis and UniProt Accession Q5JD38

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EC Tree
     2 Transferases
         2.1 Transferring one-carbon groups
             2.1.1 Methyltransferases
                2.1.1.221 tRNA (guanine9-N1)-methyltransferase
IUBMB 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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This record set is specific for:
Thermococcus kodakarensis
UNIPROT: Q5JD38
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Word Map
The taxonomic range for the selected organisms is: Thermococcus kodakarensis
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
Synonyms
trm10, trmt10a, trmt10c, trna (guanine-n(1)-)-methyltransferase, m1g9 methyltransferase, trna m1g9 methyltransferase, trna m1r9 methyltransferase, tktrm10, htrmt10a, sctrm10, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
m1R9-specific TkTrm10
-
Trm10p (ambiguous)
-
tRNA(m1G9/m1A9)-methyltransferase
-
tRNA(m1G9/m1A9)MTase
-
additional information
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) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + guanine9 in tRNAArg
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAArg
show the reaction diagram
tRNA substrate from Thermococcus kodakarensis
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAGly
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAGly
show the reaction diagram
tRNA substrate from Saccharomyces cerevisiae
-
-
?
S-adenosyl-L-methionine + guanine9 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNAPhe
show the reaction diagram
tRNA substrate from Saccharomyces cerevisiae
-
-
?
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 + guanine9 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine9 in tRNA
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0002
guanine9 in tRNAArg
pH 8.0, 50°C, recombinant enzyme, tRNA substrate from Thermococcus kodakarensis
-
0.0025
guanine9 in tRNAGly
pH 8.0, 40°C, recombinant enzyme, tRNA substrate from Saccharomyces cerevisiae
-
0.0232
guanine9 in tRNAPhe
pH 8.0, 40°C, recombinant enzyme, tRNA substrate from Saccharomyces cerevisiae
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 50
assay at, with Saccharomyces cervisiae tRNA and Thermococcus kodakarensis tRNA, respectively
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 44000, recombinant His6-atgged enzyme, SDS-PAGE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D104A
site-directed mutagenesis, the mutant shows highly reduced activity compared to wild-type
D104A/E115Q/D245A
site-directed mutagenesis, almost inactive mutant
D104N
site-directed mutagenesis, the mutant shows slightly increased 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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His6-tagged protein from Escherichia coli by nickel affinity chromatography and dialysis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene TK0422, sequence comparisons, recombinant expression of N-terminally His6-tagged protein in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team