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Information on EC 2.1.1.220 - tRNA (adenine58-N1)-methyltransferase and Organism(s) Thermus thermophilus and UniProt Accession Q8GBB2
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2.1.1.220 tRNA (adenine58-N1)-methyltransferaseIUBMB Comments
The enzyme specifically methylates adenine58 in tRNA. The methylation of A58 is critical for maintaining the stability of initiator tRNAMet in yeast .
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Word Map
- 2.1.1.220
- trnaimet
- 1-methyladenosine
- nucleoside
- mtases
-
two-subunit
-
thermus
-
exosome
-
polyadenylation
- adomet
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t-loop
- polya
- s-adenosylmethionine
-
n1-methylation
- heterotetramer
-
homotetrameric
- methionyl-trna
-
high-copy-number
- eubacteria
- methyltransferases
- s-adenosyl-l-homocysteine
-
two-component
-
s-adenosyl-l-methionine-dependent
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l-shaped
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tpsic
-
trna-binding
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hypomodified
- drug development
The taxonomic range for the selected organisms is: Thermus thermophilus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
+
adenine58 in tRNA
=
+
N1-methyladenine58 in tRNA
Synonyms
gcd14p, gcd10p, rv2118c, trna m(1)a58 methyltransferase, trm6p, rv2118p, trm61p, trm6-trm61 holoenzyme, trna (m1a58) methyltransferase, m1a58 trna methyltransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + adenine58 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
two possible mechanisms for methyl transfer: (A) with deprotonation of the amino exocyclic group of the adenine ring and via the intermediate imino tautomer of m1A, (B) by direct transfer of the methyl, without intermediate, detailed overview
PATHWAY SOURCE
PATHWAYS
-
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (adenine58-N1)-methyltransferase
The enzyme specifically methylates adenine58 in tRNA. The methylation of A58 is critical for maintaining the stability of initiator tRNAMet in yeast [3].
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
2 S-adenosyl-L-methionine + adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
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-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
S-adenosyl-L-methionine + adenine58 in tRNAGGUThr
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
the tRNA from Thermus thermophilus, that contains C60 instead of U60, is poorly methylated. Nucleoside analysis of tRNAGGUThr from the wild-type strain indicates that less than 50% of tRNAGGUThr contain m1A58
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-
?
S-adenosyl-L-methionine + adenine58 in tRNAPhe
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNAPhe
the Thermus thermophilus tRNAPhe transcript is methylated efficiently by the Thermus thermophilus enzyme, whereas the Saccharomyces cerevisiae tRNAPhe transcript is poorly methylated. Analysis of fourteen chimeric tRNA transcripts derived from these two tRNA reveals that enzyme TrmI recognized the combination of aminoacyl stem, variable region, and T-loop. TrmI methylates deltion transcripts still containing the aminoacyl stem, variable region, and T-arm. Positive sequence determinants are C56, purine 57, A58, and U60. Replacing A58 with inosine and 2-aminopurine completely abrogates methylation, demonstrating that the 6-amino group in A58 is recognized by enzyme TrmI
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-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
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-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
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-
-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
catalyzes the sitespecific formation of m1A at position 58 of the T-loop of tRNA in the absence of any other complementary protein
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-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
tRNA m1A58 methyltransferase, TrmI, catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to N1 of adenine 58 in the T-loop of tRNAs
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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
2 S-adenosyl-L-methionine + adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
tRNA m1A58 methyltransferase, TrmI, catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to N1 of adenine 58 in the T-loop of tRNAs
-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
-
-
?
S-adenosyl-L-methionine + adenine58 in tRNA
S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
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-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00013
adenine58 in tRNAPhe
pH 7.5-8.0, 55°C, wild-type Thermus thermophilus tRNAPhe as substrate
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additional information
additional information
kinetics for diverse tRNAPhe variants, overview
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additional information
additional information
-
kinetics for diverse tRNAPhe variants, overview
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the m1A58 modification occurs on (cyt)tRNAs from all three domains of life and further in (mt)tRNAs. The m1A58 MTases belong to the RFM methyltransferase superfamily, class I. In archaea and bacteria, the m1A58 MTases belong to the TrmI subfamily and function without complex partners
malfunction
physiological function
evolution
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comparative structural analysis of TrmIs from archea, prokaryota, and eukaryota, overview
physiological function
-
tRNA m1A58 methyltransferase catalyzes the transfer of a methyl group from S-adenosyl-L-methionine to N1 of adenine 58 in the T-loop of tRNAs, a modification, that is essential for cell growth at high temperatures
additional information
malfunction
inactivation of the Thermus thermophilus trmI gene results in a thermosensitive phenotype (growth defect at 80°C)
malfunction
the lack of the enzyme forming m1A58 leads to thermosensitivity in bacterial tRNAs
physiological function
role of the N1-methylation of tRNA adenosine-58 in adaptation of life to extreme temperatures
physiological function
the m1A58 modifications have both been linked to structural stability and/or correct folding of the tRNA and is related to structural thermostability of tRNA. The combination of m1A58 with two other post-transcriptional modifications (Gm18 and m5s2U54) increases the melting temperature of tRNAs from Thermus thermophilus by approximately 10°C compared to the unmodified transcript
additional information
recognition of tRNA substrate and structure of the catalytic pocket, overview. The flexibility of the N-terminal domain that is probably important to bind tRNA. Role of residue Y78 in stabilizing the conformation of the A58 ribose needed to hold substrate adenosine in the active site, and central role of residue D170 in binding the amino moiety of S-adenosyl-L-methionine and the exocyclic amino group of adenine
additional information
catalytic mechanism of m1A58 specific RFM family member TrmI, overview. The conserved aspartate residue (Asp181) is essential for m1A58 MTase activity in Thermus thermophilus
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28582
4 * 28582, calculation from sequence, composed of two types of subunits (Gcd14p and Gcd10p)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
bacterial and archaeal TrmI proteins have been shown to form homotetramers. Each homotetramers accomodates up to two tRNA molecules
tetramer
tetramer
-
dimers of tightly assembled dimers, bacterial enzymes from thermophilic organisms display additional intermolecular ionic interactions across the dimer interfaces, interactions and structure analysis, overview
additional information
-
comparative structural analysis of TrmIs, overview
tetramer
4 * 28582, calculation from sequence, composed of two types of subunits (Gcd14p and Gcd10p)
tetramer
the enzyme remains tetrameric upon tRNA binding, with formation of complexes involving one to two molecules of tRNA per TrmI tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme mutant D170A and Y78A in complex with S-adenosyl-L-methionine, hanging drop vapor diffusion method, mixing of 10 mg/ml protein in 20 mM Tris-HCl buffer, pH 8.0, 100 mM KCl, and 2mM S-adenosyl-L-methionine with reservoir solution containing 2.4 M ammonium sulfate and 10% v/v isopropanol for mutant D170A and 2.1 M ammonium sulfate and 8% v/v isopropanol for mutant Y78A, X-ray diffraction structure determination and analysis at 3.1 A and 2.6 A resolution, respectively. Crystallization assays of enzyme TrmI Y194A lead to poorly diffracting crystals
sitting-drop vapor-diffusion method at 19°C. Crystal structure of TrmI, in complex with S-adenosyl-L-homocysteine, is determined at 1.7 A resolution. The conserved residues that form the catalytic cavity (D170, Y78, and Y194) are essential for fashioning an optimized shape of the catalytic pocket
TrmI protein complexed with S-adenosyl-L-homocysteine, X-ray diffraction structure determination and analysis at 1.7 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D170A
site-directed mutagenesis, mutation of a conserved active site residue
Y194A
site-directed mutagenesis, crystallization assays of TrmI Y194A lead to poorly diffracting crystals
Y78A
site-directed mutagenesis, mutation of a conserved active site residue. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine, as compared to the wild-type structure. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Droogmans, L.; Roovers, M.; Bujnicki, J.M.; Tricot, C.; Hartsch, T.; Stalon, V.; Grosjean, H.
Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures
Nucleic Acids Res.
31
2148-2156
2003
Thermus thermophilus (Q8GBB2), Thermus thermophilus, Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 (Q8GBB2)
Barraud, P.; Golinelli-Pimpaneau, B.; Atmanene, C.; Sanglier, S.; Van Dorsselaer, A.; Droogmans, L.; Dardel, F.; Tisne, C.
Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA
J. Mol. Biol.
377
535-550
2008
Thermus thermophilus (Q8GBB2), Thermus thermophilus
Guelorget, A.; Barraud, P.; Tisne, C.; Golinelli-Pimpaneau, B.
Structural comparison of tRNA m(1)A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions
BMC Struct. Biol.
11
48
2011
Aquifex aeolicus, Homo sapiens, Mycobacterium tuberculosis, Pyrococcus abyssi, Saccharomyces cerevisiae, Thermotoga maritima, Thermus thermophilus
Degut, C.; Ponchon, L.; Folly-Klan, M.; Barraud, P.; Tisne, C.
The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI
Biophys. Chem.
210
27-34
2016
Thermus thermophilus (Q8GBB2), Thermus thermophilus DSM 7039 (Q8GBB2)
Takuma, H.; Ushio, N.; Minoji, M.; Kazayama, A.; Shigi, N.; Hirata, A.; Tomikawa, C.; Ochi, A.; Hori, H.
Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI)
J. Biol. Chem.
290
5912-5925
2015
Thermus thermophilus (Q8GBB2), Thermus thermophilus, Thermus thermophilus DSM 7039 (Q8GBB2)
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