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Information on EC 2.1.1.219 - tRNA (adenine57-N1/adenine58-N1)-methyltransferase and Organism(s) Pyrococcus abyssi and UniProt Accession Q9V1J7
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2.1.1.219 tRNA (adenine57-N1/adenine58-N1)-methyltransferaseIUBMB Comments
The enzyme catalyses the formation of N1-methyladenine at two adjacent positions (57 and 58) in the T-loop of certain tRNAs (e.g. tRNAAsp). Methyladenosine at position 57 is an obligatory intermediate for the synthesis of methylinosine, which is commonly found at position 57 of archaeal tRNAs.
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Word Map
- 2.1.1.219
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pyrococcus
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avermitilis
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t-loop
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putidaredoxin
- s-adenosyl-l-homocysteine
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ferredoxins
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region-specific
The taxonomic range for the selected organisms is: Pyrococcus abyssi
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
2
+
=
2
+
2
+
adenine57/adenine58 in tRNA
=
2
+
N1-methyladenine57/N1-methyladenine58 in tRNA
Synonyms
pabtrmi, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (adenine57/adenine58-N1)-methyltransferase
The enzyme catalyses the formation of N1-methyladenine at two adjacent positions (57 and 58) in the T-loop of certain tRNAs (e.g. tRNAAsp). Methyladenosine at position 57 is an obligatory intermediate for the synthesis of methylinosine, which is commonly found at position 57 of archaeal tRNAs.
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 + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNAArg
2 S-adenosyl-L-homocysteine + adenine57/N1-methyladenine58 in tRNAArg
modified mini-tRNAAsp substrate, PabTrmI recognizes and methylates only A58 in mini-tRNAArgTCT containing the G57A58A59U60 sequence
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-
?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNAAsp
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNAAsp
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
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-
-
?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
the solvent accessibility of the S-adenosyl-L-methionine pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by S-adenosyl-L-methionine without prior release of monomethylated tRNA
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-
?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNAAsp
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNAAsp
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-
-
?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNAAsp
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNAAsp
the presence of adenine at position 59 in Pyrococcus abyssi tRNA(Asp) is important for the multi-site specificity of the archaeal enzyme at both positions 57 and 58 in tRNAAsp. His78 near the active site is important for efficient catalysis
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?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNAAsp
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNAAsp
modified mini-tRNAAsp substrate, PabTrmI recognizes and methylates both A57 and A58 in mini-tRNAAsp containing the A57A58A59U60 sequence
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?
additional information
?
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methylation occurs at position 58 when position 57 contains a methylated adenine, an adenine derivative or guanine, whereas the methylation at position 57 strictly requires adenine 58 to proceed efficiently. This supports our previous conclusion that A57 is methylated before A58 in tRNAs containing the A57A58A59 sequence
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?
additional information
?
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methylation occurs at position 58 when position 57 contains a methylated adenine, an adenine derivative or guanine, whereas the methylation at position 57 strictly requires adenine 58 to proceed efficiently. This supports our previous conclusion that A57 is methylated before A58 in tRNAs containing the A57A58A59 sequence
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?
additional information
?
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in most organisms, the widely conserved 1-methyladenosine58 (m1A58) tRNA modification is catalyzed by S-adenosyl-L-methionine-dependent site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation, multi-site specificity mechanism, overview
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?
additional information
?
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in most organisms, the widely conserved 1-methyladenosine58 (m1A58) tRNA modification is catalyzed by S-adenosyl-L-methionine-dependent site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation, multi-site specificity mechanism, overview
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-
?
additional information
?
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construction of three oligoribonucleotide substrates of Pyrococcus abyssi TrmI containing a fluorescent 2-aminopurine at the two target positions 57 and 58, analysis of RNA binding kinetics and methylation reactions by stopped-flow and mass spectrometry, overview. PabTrmI does not modify 2-aminopurine but methylates the adjacent target adenine. 2-Aminopurine seriously impairs the methylation of A57 but not A58, confirming that PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence
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?
additional information
?
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construction of three oligoribonucleotide substrates of Pyrococcus abyssi TrmI containing a fluorescent 2-aminopurine at the two target positions 57 and 58, analysis of RNA binding kinetics and methylation reactions by stopped-flow and mass spectrometry, overview. PabTrmI does not modify 2-aminopurine but methylates the adjacent target adenine. 2-Aminopurine seriously impairs the methylation of A57 but not A58, confirming that PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence
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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 + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
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-
-
?
2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA
2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
the solvent accessibility of the S-adenosyl-L-methionine pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by S-adenosyl-L-methionine without prior release of monomethylated tRNA
-
-
?
additional information
?
-
in most organisms, the widely conserved 1-methyladenosine58 (m1A58) tRNA modification is catalyzed by S-adenosyl-L-methionine-dependent site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation, multi-site specificity mechanism, overview
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-
?
additional information
?
-
-
in most organisms, the widely conserved 1-methyladenosine58 (m1A58) tRNA modification is catalyzed by S-adenosyl-L-methionine-dependent site-specific enzyme TrmI. In archaea, TrmI also methylates the adjacent adenine 57, m1A57 being an obligatory intermediate of 1-methyl-inosine57 formation, multi-site specificity mechanism, overview
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
dynamics of RNA binding by PabTrmI in the presence and absence of S-adenosyl-L-methionine
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
steady-state fluorescent assay and stopped-flow kinetics with 2-aminopurine-modifed tRNA substrates, , overview
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additional information
additional information
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steady-state fluorescent assay and stopped-flow kinetics with 2-aminopurine-modifed tRNA substrates, , 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
additional information
additional information
PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence. m1A58 formation triggers RNA release. A model of the protein-tRNA complex shows both target adenines in proximity of S-adenosyl-L-methionine and emphasizes no major tRNA conformational change except base flipping during the reaction. The solvent accessibility of the S-adenosyl-L-methionine pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by S-adenosyl-L-methionine without prior release of monomethylated tRNA. Dynamics of RNA binding by PabTrmI in the presence and absence of S-adenosyl-L-methionine, structural model of PabTrmI in complex with tRNA, overview
additional information
-
PabTrmI methylates efficiently the first adenine of the A57A58A59 sequence. m1A58 formation triggers RNA release. A model of the protein-tRNA complex shows both target adenines in proximity of S-adenosyl-L-methionine and emphasizes no major tRNA conformational change except base flipping during the reaction. The solvent accessibility of the S-adenosyl-L-methionine pocket is not affected by the tRNA, thereby enabling S-adenosyl-L-homocysteine to be replaced by S-adenosyl-L-methionine without prior release of monomethylated tRNA. Dynamics of RNA binding by PabTrmI in the presence and absence of S-adenosyl-L-methionine, structural model of PabTrmI in complex with tRNA, overview
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
concentrated by ultrafiltration, crystallisation at 20°C by the sitting-drop vapour diffusion method
crystal structure TrmI in complex with SAH is determined in two different space groups at 2.6 and 2.05 A resolution, and in complex with S-adenosyl-L-methionine (SAM) at 1.6 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C196S/C233S
mutant enzyme C196S/C233S is inactivated at 85°C after 20 min, wild-type enzyme is stable for more than 1 h
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
85
mutant enzyme C196S/C233S is inactivated after 20 min, wild-type enzyme is stable for more than 1 h
additional information
additional information
the stabilisation of Pyrococcus abyssi TrmI at extreme temperatures involves intersubunit disulfide bridges formed between Cys196 and Cys233 that reinforce the tetrameric oligomerisation
additional information
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the stabilisation of Pyrococcus abyssi TrmI at extreme temperatures involves intersubunit disulfide bridges formed between Cys196 and Cys233 that reinforce the tetrameric oligomerisation
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant C-terminally His6-tagged enzyme by nickel affiniyt chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Roovers, M.; Wouters, J.; Bujnicki, J.M.; Tricot, C.; Stalon, V.; Grosjean, H.; Droogmans, L.
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase
Nucleic Acids Res.
32
465-476
2004
Pyrococcus abyssi (Q9V1J7), Pyrococcus abyssi, Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543 (Q9V1J7)
Guelorget, A.; Roovers, M.; Gurineau, V.; Barbey, C.; Li, X.; Golinelli-Pimpaneau, B.
Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase
Nucleic Acids Res.
38
6206-6218
2010
Pyrococcus abyssi (Q9V1J7), Pyrococcus abyssi
Hamdane, D.; Guelorget, A.; Gurineau, V.; Golinelli-Pimpaneau, B.
Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase
Nucleic Acids Res.
42
11697-11706
2015
Pyrococcus abyssi (Q9V1J7), Pyrococcus abyssi, Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543 (Q9V1J7)
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