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Literature summary for 2.1.1.228 extracted from

  • Urbonavicius, J.; Rutkiene, R.; Lopato, A.; Tauraite, D.; Stankeviciute, J.; Aucynaite, A.; Kaliniene, L.; van Tilbeurgh, H.; Meskys, R.
    Evolution of tRNAPhe imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea (2016), RNA, 22, 1871-1883 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of His-tagged enzyme Nanoarchaeum equitans
recombinant expression of His-tagged wild-type and mutant enzymes Pyrococcus abyssi

Protein Variants

Protein Variants Comment Organism
E173A site-directed mutagenesis, the mutant shows 9 and 26% of wild-type activity for imG and imG2 formation, respectively Pyrococcus abyssi
E213A site-directed mutagenesis, inactive mutant Pyrococcus abyssi
F165A site-directed mutagenesis, inactive mutant Pyrococcus abyssi
P260N site-directed mutagenesis, the mutant shows no and 114% of wild-type activity for imG and imG2 formation, respectively Pyrococcus abyssi
P262A site-directed mutagenesis, the mutant shows 5 and 8% of wild-type activity for imG and imG2 formation, respectively Pyrococcus abyssi
R134A site-directed mutagenesis, the mutant shows 2 and 4% of wild-type activity for imG and imG2 formation, respectively Pyrococcus abyssi
R174A site-directed mutagenesis, the mutant shows 8 and 69% of wild-type activity for imG and imG2 formation, respectively Pyrococcus abyssi

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Pyrococcus abyssi
Mg2+ required Nanoarchaeum equitans

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
S-adenosyl-L-methionine + 4-demethylwyosine Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine Nanoarchaeum equitans
-
S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine Pyrococcus abyssi Orsay
-
S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine Nanoarchaeum equitans
-
S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine Pyrococcus abyssi Orsay
-
S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
-
?
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe Nanoarchaeum equitans
-
S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
-
?
S-adenosyl-L-methionine + guanine37 in tRNA Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?
S-adenosyl-L-methionine + guanine37 in tRNA Nanoarchaeum equitans
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?
S-adenosyl-L-methionine + guanine37 in tRNA Pyrococcus abyssi Orsay
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?

Organism

Organism UniProt Comment Textmining
Nanoarchaeum equitans Q74NE4
-
-
Pyrococcus abyssi Q9V2G1
-
-
Pyrococcus abyssi Orsay Q9V2G1
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant expression of His-tagged enzyme by affinity chromatography and desalting gel filtration Nanoarchaeum equitans
recombinant expression of His-tagged wild-type and mutant enzymes to near homogeneity by 20 min heat treatment at 70°C and 65°C, respectively, followed by affinity chromatography and desalting gel filtration Pyrococcus abyssi

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information Nanoarchaeum equitans NEQ228 protein displays a dual tRNAPhe:m1G/imG2 methyltransferase activity. Two different types of substrates are used: (1) bulk tRNA, isolated from Salmonella enterica trmDELTA27 mutant containing the unmodified G37 nucleotide leading tothe formation of pm1G, and (2) tRNA, which is isolated from the Saccharomes cerevisiae DELTAtyw2 mutant that contains the imG-14 wyosine derivative leading to formation of pimG2pA dinucleotide and to a lesser extent to pm1G, likely resulting from the small amounts of G37-containing tRNAPhe present in the bulk tRNA isolates from the Scetyw2 mutant Nanoarchaeum equitans ?
-
-
additional information Pyrococcus abyssi PAB2272 protein displays a dual tRNAPhe:m1G/imG2 methyltransferase activity. Two different types of substrates are used: (1) bulk tRNA, isolated from Salmonella enterica trmDELTA27 mutant containing the unmodified G37 nucleotide leading to the formation of pm1G, and (2) tRNA, which is isolated from the Saccharomes cerevisiae DELTAtyw2 mutant that contains the imG-14 wyosine derivative leading to formation of pimG2pA dinucleotide and to a lesser extent to pm1G, likely resulting from the small amounts of G37-containing tRNAPhe present in the bulk tRNA isolates from the Scetyw2 mutant Pyrococcus abyssi ?
-
-
additional information Pyrococcus abyssi PAB2272 protein displays a dual tRNAPhe:m1G/imG2 methyltransferase activity. Two different types of substrates are used: (1) bulk tRNA, isolated from Salmonella enterica trmDELTA27 mutant containing the unmodified G37 nucleotide leading to the formation of pm1G, and (2) tRNA, which is isolated from the Saccharomes cerevisiae DELTAtyw2 mutant that contains the imG-14 wyosine derivative leading to formation of pimG2pA dinucleotide and to a lesser extent to pm1G, likely resulting from the small amounts of G37-containing tRNAPhe present in the bulk tRNA isolates from the Scetyw2 mutant Pyrococcus abyssi Orsay ?
-
-
S-adenosyl-L-methionine + 4-demethylwyosine
-
Pyrococcus abyssi S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine
-
Nanoarchaeum equitans S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine i.e. im-G14, activity of EC 2.1.1.282 Pyrococcus abyssi S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine i.e. im-G14, activity of EC 2.1.1.282 Nanoarchaeum equitans S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine
-
Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 4-demethylwyosine i.e. im-G14, activity of EC 2.1.1.282 Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + isowyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine
-
Pyrococcus abyssi S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine
-
Nanoarchaeum equitans S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine i.e. yW-86, activity of EC 2.1.1.228 Pyrococcus abyssi S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine i.e. yW-86, activity of EC 2.1.1.228 Nanoarchaeum equitans S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-aminocarboxypropyl-demethylwyosine
-
Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + wyosine
-
?
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe
-
Pyrococcus abyssi S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
-
?
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe
-
Nanoarchaeum equitans S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
Pyrococcus abyssi S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
Nanoarchaeum equitans S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
Pyrococcus abyssi Orsay S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?

Synonyms

Synonyms Comment Organism
aTrm5a methyltransferase
-
Pyrococcus abyssi
aTrm5a methyltransferase
-
Nanoarchaeum equitans
aTrm5a/Taw22-like enzyme
-
Pyrococcus abyssi
More see also EC 2.1.1.282 Pyrococcus abyssi
More see also EC 2.1.1.282 Nanoarchaeum equitans
NEQ228
-
Nanoarchaeum equitans
PAB2272
-
Pyrococcus abyssi
TAW22
-
Pyrococcus abyssi
TAW22
-
Nanoarchaeum equitans
Trm5a
-
Pyrococcus abyssi
Trm5a
-
Nanoarchaeum equitans
Trm5a/Taw22-like enzyme
-
Nanoarchaeum equitans
tRNAPhe:imG2 methyltransferase
-
Pyrococcus abyssi
tRNAPhe:imG2 methyltransferase
-
Nanoarchaeum equitans

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
50
-
assay at Pyrococcus abyssi
50
-
assay at Nanoarchaeum equitans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Pyrococcus abyssi
8
-
assay at Nanoarchaeum equitans

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine
-
Pyrococcus abyssi
S-adenosyl-L-methionine
-
Nanoarchaeum equitans

General Information

General Information Comment Organism
evolution archaeal Trm5a, a member of the archaeal Trm5a/b/c family of enzymes involved in the biosynthesis of the wyosine derivatives, division of the family aTrm5 into three subfamilies aTrm5a (further divided into Taw21 and Taw22 which are monofunctional and bifunctional aTrm5a), aTrm5b, and aTrm5c. While the enzymes belonging to these subfamilies do not significantly differ in their AdoMet-binding site, small differences have been observed within the NPPY motif, which, in certain amino-methyltransferases, is involved in the positioning of the target nitrogen atom. In contrast, the N-terminal sequences of the aforementioned enzymes differ substantially, e.g. a small conservative domain called D1 is present in aTrm5b and aTrm5c but absent in most of the aTrm5a proteins. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. Amino acid sequence alignment of Trm5a/b/c family of proteins. Monofunctional and bifunctional aTrm5a enzymes, overview Nanoarchaeum equitans
evolution archaeal Trm5a, a member of the archaeal Trm5a/b/c family of enzymes involved in the biosynthesis of the wyosine derivatives, division of the family aTrm5 into three subfamilies aTrm5a (further divided into Taw21 and Taw22 which are monofunctional and bifunctional aTrm5a), aTrm5b, and aTrm5c. While the enzymes belonging to these subfamilies do not significantly differ in their AdoMet-binding site, small differences have been observed within the NPPY motif, which, in certain amino-methyltransferases, is involved in the positioning of the target nitrogen atom. In contrast, the N-terminal sequences of the aforementioned enzymes differ substantially, e.g. a small conservative domain called D1 is present in aTrm5b and aTrm5c but absent in most of the aTrm5a proteins. Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. Amino acid sequence alignment of Trm5a/b/c/ family of proteins. Monofunctional and bifunctional aTrm5a enzymes, overview Pyrococcus abyssi
malfunction substitutions of individual conservative amino acids of Pyrococcus abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37 Pyrococcus abyssi
malfunction substitutions of individual conservative amino acids of Pyrococcus abyssi Taw22 (P260N, E173A, and R174A) have a differential effect on the formation of m1G/imG2, while replacement of R134, F165, E213, and P262 with alanine abolishes the formation of both derivatives of G37 Nanoarchaeum equitans
metabolism putative enzymatic pathway leading to the formation of wyosine derivatives in Archaea Pyrococcus abyssi
metabolism putative enzymatic pathway leading to the formation of wyosine derivatives in Archaea Nanoarchaeum equitans
physiological function tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe. In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. Methyltransferase aTrm5a/Taw22 likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G (EC 2.1.1.228), and C7-methylation of imG-14 to yield imG2 (EC 2.1.1.282) Pyrococcus abyssi
physiological function tricyclic wyosine derivatives are found at position 37 of eukaryotic and archaeal tRNAPhe. In Archaea, the intermediate imG-14 is targeted by three different enzymes that catalyze the formation of yW-86, imG, and imG2. Methyltransferase aTrm5a/Taw22 likely catalyzes two distinct reactions: N1-methylation of guanosine to yield m1G (EC 2.1.1.228), and C7-methylation of imG-14 to yield imG2 (EC 2.1.1.282) Nanoarchaeum equitans