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Information on EC 2.1.1.218 - tRNA (adenine9-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
                2.1.1.218 tRNA (adenine9-N1)-methyltransferase
IUBMB 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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This record set is specific for:
Thermococcus kodakarensis
UNIPROT: Q5JD38
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The taxonomic range for the selected organisms is: Thermococcus kodakarensis
The expected taxonomic range for this enzyme is: Eukaryota, Archaea, Bacteria
Reaction Schemes
hide
S-adenosyl-L-methionine
+
adenine9 in tRNA
=
S-adenosyl-L-homocysteine
+
N1-methyladenine9 in tRNA
+
adenine9 in tRNA
=
+
N1-methyladenine9 in tRNA
Synonyms
trmt10b, htrmt10b, adenosine-specific trm10, 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 (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).
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 + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + adenine9 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAPhe
show the reaction diagram
tRNA substrate from Saccharomyces cerevisiae
-
-
?
S-adenosyl-L-methionine + adenine9 in tRNAThr
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAThr
show the reaction diagram
tRNA substrate from Thermococcus kodakarensis
-
-
?
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 + adenine9 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine9 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
no activity is detected in the absence of metal
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
enzyme kinetic analysis and modeling
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
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
-
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
pH-rate profiles for the two activities catalyzed by the bifunctional methyltransferase TkTrm10, cf. EC 2.1.1.221
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
malfunction
mutation of catalytic residue Asp206 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
additional information
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 44000, recombinant His6-tagged enzyme, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure PDB ID 5A7T
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
Sulfolobus acidocaldarius (Q4J894), 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), Sulfolobus acidocaldarius (Q4J894), Sulfolobus acidocaldarius ATCC 33909 (Q4J894), Sulfolobus acidocaldarius DSM 639 (Q4J894), Sulfolobus acidocaldarius JCM 8929 (Q4J894), Sulfolobus acidocaldarius NBRC 15157 (Q4J894), Sulfolobus acidocaldarius NCIMB 11770 (Q4J894), 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 ATCC BAA-918 (Q5JD38)
Manually annotated by BRENDA team