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Literature summary for 2.1.1.35 extracted from

  • Walbott, H.; Leulliot, N.; Grosjean, H.; Golinelli-Pimpaneau, B.
    The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity (2008), Nucleic Acids Res., 36, 4929-4940.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

Crystallization (Comment) Organism
native and selenomethionylated purified enzyme PabTrmU54 in complex with S-adenosyl-L-homocysteine, hanging-drop by vapor diffusion method, 0.001 ml of a mixture of protein and S-adenosyl-L-methionine in a 1:2 molar ratiomixed with 0.001 ml of 0.6 ml reservoir solution containing 15% PEG 8000, 0.05 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6,18°C, few days, X-ray diffraction structure determination and analysi at 1.9 A resolution, molecular replacement, modelling Pyrococcus abyssi

Metals/Ions

Metals/Ions Comment Organism Structure
additional information the enzyme might contain a [Fe4S4] cluster, overview Pyrococcus abyssi

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Pyrococcus abyssi the enzyme emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea ?
-
?
S-adenosyl-L-methionine + tRNA containing uridine at position 54 Pyrococcus abyssi
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S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
-
?

Organism

Organism UniProt Comment Textmining
Pyrococcus abyssi Q9UZR7
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-

Purification (Commentary)

Purification (Comment) Organism
native and selenomethionylated enzyme by nickel affinity chromatography Pyrococcus abyssi

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the enzyme emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea Pyrococcus abyssi ?
-
?
additional information structure-function analysis using mini-tRNA stem-loop, overview Pyrococcus abyssi ?
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?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
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Pyrococcus abyssi S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
-
?
S-adenosyl-L-methionine + tRNA containing uridine at position 54 the enzyme purified under aerobic conditions is specific for tRNA but not rRNA, and specifically modifies the U54 position in the T-C loop of yeast tRNAAsp. A tRNA lacking both the D and anticodon stem-loops is recognized by PabTrmU54 Pyrococcus abyssi S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54 The adenine ring of S-adenosyl-L-homocysteine makes van der Waals and hydrophobic interactions with residues S300 and Y278. The sugar ring of S-adenosyl-L-homocysteine stacks on P342 whereas its two oxygen atoms form H-bonds with the carboxylate group of D299. The terminal carboxylate of the homocysteine moiety is hydrogen bonded to the hydroxyl group of T283 and the amide side chain of Q252 ?

Subunits

Subunits Comment Organism
More the enzyme contains an N-terminal TRAM domain, structure-function analysis, overview Pyrococcus abyssi

Synonyms

Synonyms Comment Organism
PabTrmU54
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Pyrococcus abyssi
S-adenosyl-L-methionine-dependent tRNA (uracil-54, C5)-methyltransferase
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Pyrococcus abyssi
tRNA (uracil-54, C5)-methyltransferase
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Pyrococcus abyssi

Temperature Optimum [°C]

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

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.2
-
assay at Pyrococcus abyssi

Cofactor

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