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Information on EC 2.1.1.218 - tRNA (adenine9-N1)-methyltransferase and Organism(s) Sulfolobus acidocaldarius and UniProt Accession Q4J894

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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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Sulfolobus acidocaldarius
UNIPROT: Q4J894
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The taxonomic range for the selected organisms is: Sulfolobus acidocaldarius
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
adenosine-specific Trm10
-
tRNA m1A9-methyltransferase
-
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 tRNAiMet
S-adenosyl-L-homocysteine + N1-methyladenine9 in tRNAiMet
show the reaction diagram
docking model of tRNAiMet of Sulfolobus acidocaldarius onto SaTrm10-SAH
-
-
?
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 for activity, best at 5 mM
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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 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
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35000
native enzyme, gel filtration
38000
recombinant His-tagged enzyme, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure PDB ID 5A7T
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression 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
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
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)
Manually annotated by BRENDA team