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Literature summary extracted from

  • Auxilien, S.; Rasmussen, A.; Rose, S.; Brochier-Armanet, C.; Husson, C.; Fourmy, D.; Grosjean, H.; Douthwaite, S.
    Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases (2011), RNA, 17, 45-53.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.35 expressed in Escherichia coli as a His-tagged fusion protein Pyrococcus abyssi

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.1.1.35 Mg2+ stimulating effect Pyrococcus abyssi

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
 ?
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA Pyrococcus abyssi
-
 S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
 ?
2.1.1.190 S-adenosyl-L-methionine + uracil1939 in 23S rRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.35 Pyrococcus abyssi
-
 the genome of the hyperthermophilic archaeon Pyrococcus abyssi contains two open reading frames, PAB0719 and PAB0760,which are shownby comparative phylogenetic analyses to belong to the COG2265 m5U methyltransferases
-
2.1.1.189 Escherichia coli
-
 gene rlmC
-
2.1.1.189 Pyrococcus abyssi
-
-
-
2.1.1.190 Escherichia coli
-
 gene rlmD
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.1.1.35 using Ni-NTA chromatography Pyrococcus abyssi

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.35 additional information recombinant PAB0719 is shown to function like TrmA from Escherichia coli and catalyzes m5U formation at position 54 in Pyrococcus abyssi tRNAs Pyrococcus abyssi ?
-
 ?
2.1.1.189 additional information substrate specificity, overview Pyrococcus abyssi ?
-
 ?
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
 ?
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA
-
 Pyrococcus abyssi S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
 ?
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA PAB0760 is a m5U methyltransferase and recognizes a specific uridine within the loop of 23S rRNA hairpin 35 in a highly specific manner Pyrococcus abyssi S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA product identification by reverse transcriptase primer extension and MALDI mass spectrometry ?
2.1.1.189 S-adenosyl-L-methionine + uracil747 in 23S rRNA RlmC recognizes a specific uridine within the loop of 23S rRNA hairpin 35 Escherichia coli S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA
-
 ?
2.1.1.190 S-adenosyl-L-methionine + uracil1939 in 23S rRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
-
 ?
2.1.1.190 S-adenosyl-L-methionine + uracil1939 in 23S rRNA rRNA substrate structure, overview Escherichia coli S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.1.1.35 PAB0719
-
 Pyrococcus abyssi
2.1.1.189 m5U methyltransferase
-
 Escherichia coli
2.1.1.189 m5U methyltransferase
-
 Pyrococcus abyssi
2.1.1.189 PAB0760
-
 Pyrococcus abyssi
2.1.1.189 RlmC
-
 Escherichia coli
2.1.1.189 RumB formerly Escherichia coli
2.1.1.190 m5U methyltransferase
-
 Escherichia coli
2.1.1.190 RlmD
-
 Escherichia coli
2.1.1.190 RNA m5U methyltransferase
-
 Escherichia coli
2.1.1.190 RumA formerly Escherichia coli

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.1.1.35 80
-
 kinetics of m5U formation by PAB0760 proceed faster at 80°C than at 50°C Pyrococcus abyssi

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.1.1.35 7.5
-
 assay at Pyrococcus abyssi

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.35 S-adenosyl-L-methionine
-
 Pyrococcus abyssi
2.1.1.189 S-adenosyl-L-methionine
-
 Pyrococcus abyssi
2.1.1.190 S-adenosyl-L-methionine
-
 Escherichia coli

General Information

EC Number General Information Comment Organism
2.1.1.189 evolution PAB0760 originates as RlmD-type m5U methyltransferase and undergoes changes in target specificity after its acquisition by a Thermococcales ancestor from a bacterial source. PAB0760 possesses bacterial RlmC-like activity and specifically methylates the nucleotide equivalent to U747 in Pyrococcus abyssi 23S rRNA, but with a sequence most closely related to the bacterial RlmD, the archetypical enzyme that is specific for m5U1939 in 23S rRNA Pyrococcus abyssi
2.1.1.190 physiological function RlmD is the archetypical enzyme that is specific for m5U1939 in 23S rRNA Escherichia coli