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Literature summary for 2.1.1.282 extracted from

  • Wang, C.; Jia, Q.; Zeng, J.; Chen, R.; Xie, W.
    Structural insight into the methyltransfer mechanism of the bifunctional Trm5 (2017), Sci. Adv., 3, e1700195 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene trm5a, recombinant expression of wild-type and mutant enzymes Pyrococcus abyssi

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant apo-PaTrm5a and PaTrm5a in complex with tRNAPhe, and PaTrm5a-tRNAPhe (imG-14)-SAH ternary complex, X-ray diffraction structure determination and analysis Pyrococcus abyssi

Protein Variants

Protein Variants Comment Organism
D243A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
E213A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
H128A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
R133A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
R135A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
R174A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi
Y318A site-directed mutagenesis, substrate binding compared to wild-type enzyme Pyrococcus abyssi

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Pyrococcus abyssi

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Pyrococcus abyssi bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively) ?
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S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe Pyrococcus abyssi
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S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
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?

Organism

Organism UniProt Comment Textmining
Pyrococcus abyssi Q9V2G1
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-

Purification (Commentary)

Purification (Comment) Organism
recombinant wild-type and mutant enzymes Pyrococcus abyssi

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively) Pyrococcus abyssi ?
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additional information structural basis for substrate recognition, the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA., the enzyme recognizes the overall shape of tRNA. PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Enzyme-substrate interactions in the catalytic domain. The anticodon interactions mostly concentrate on the A36-G37-A38 triplet. Proposed reaction mechanism of Trm5a with modified yeast tRNAPhe, overview Pyrococcus abyssi ?
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S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe
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Pyrococcus abyssi S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
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?
S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe imG-14 Pyrococcus abyssi S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
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?

Subunits

Subunits Comment Organism
More substrate interactions with the catalytic region in the PaTrm5a-tRNAPhe-(imG-14)-SAH ternary complex, overview. In the model, imG-14 is flipped into a hydrophobic pocket formed by Phe165, Phe284, Tyr318, Met170, Tyr197, and the 260PTPK263 fragment Pyrococcus abyssi

Synonyms

Synonyms Comment Organism
More see also EC 2.1.1.228 Pyrococcus abyssi
PaTrm5a
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Pyrococcus abyssi
TAW22
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Pyrococcus abyssi
Trm5a
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Pyrococcus abyssi

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
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assay at Pyrococcus abyssi

pH Optimum

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

Cofactor

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

General Information

General Information Comment Organism
malfunction deletion of the D1 domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate Pyrococcus abyssi
additional information structure comparison of the Pyrococcus abyssii Trm5a enzyme structure (PDB ID 5WT1) with the structure of its orthologue Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii, overview Pyrococcus abyssi
physiological function the methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m1G37 (EC 2.1.1.228) and imG2 (EC 2.1.1.282), two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates Pyrococcus abyssi