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Information on EC 2.1.1.35 - tRNA (uracil54-C5)-methyltransferase and Organism(s) Pyrococcus abyssi and UniProt Accession Q9UZR7
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2.1.1.35 tRNA (uracil54-C5)-methyltransferaseIUBMB Comments
Unlike this enzyme, EC 2.1.1.74 (methylenetetrahydrofolate---tRNA-(uracil54-C5)-methyltransferase (FADH2-oxidizing)), uses 5,10-methylenetetrahydrofolate and FADH2 to supply the atoms for methylation of U54 .
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The taxonomic range for the selected organisms is: Pyrococcus abyssi
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
+
uracil54 in tRNA
=
+
5-methyluracil54 in tRNA
Synonyms
rtase, trmt2a, trna(m5u54)methyltransferase, pab0719, ribothymidyl synthase, pab0719 enzyme, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
S-adenosyl-L-methionine-dependent tRNA (uracil-54, C5)-methyltransferase
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m5U-methyltransferase
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-
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methyltransferase, transfer ribonucleate uracil 5-
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ribothymidyl synthase
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rTase
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RUMT
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transfer RNA uracil 5-methyltransferase
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transfer RNA uracil methylase
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tRNA uracil 5-methyltransferase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
methyl group transfer
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (uracil54-C5)-methyltransferase
Unlike this enzyme, EC 2.1.1.74 (methylenetetrahydrofolate---tRNA-(uracil54-C5)-methyltransferase (FADH2-oxidizing)), uses 5,10-methylenetetrahydrofolate and FADH2 to supply the atoms for methylation of U54 [4].
CAS REGISTRY NUMBER
COMMENTARY
37257-02-6
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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
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
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-
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?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine 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
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
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?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
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-
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?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
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PAB0719 enzyme or PabTrmU54 displays an identical specificity to eucaryontal homologue TrmA, as it catalyses the in vitro formation of m5U-54 in tRNA
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?
additional information
?
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the enzyme emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea
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?
additional information
?
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structure-function analysis using mini-tRNA stem-loop, overview
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?
additional information
?
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recombinant PAB0719 is shown to function like TrmA from Escherichia coli and catalyzes m5U formation at position 54 in Pyrococcus abyssi tRNAs
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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
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
-
-
-
?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
-
-
-
-
?
additional information
?
-
the enzyme emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
the enzyme might contain a [Fe4S4] cluster, overview
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
80
-
kinetics of m5U formation by PAB0760 proceed faster at 80°C than at 50°C
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
the enzyme contains an N-terminal TRAM domain, structure-function analysis, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native and selenomethionylated enzyme by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
genes PAB0719 and PAB0760, DNA and amino acid sequence determination and analysis, detailed phylogenetic analysis, expression in Escherichia coli strain BL21(DE3)
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Urbonavicius, J.; Auxilien, S.; Walbott, H.; Trachana, K.; Golinelli-Pimpaneau, B.; Brochier-Armanet, C.; Grosjean, H.
Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer
Mol. Microbiol.
67
323-335
2008
Pyrococcus abyssi
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
Nucleic Acids Res.
36
4929-4940
2008
Pyrococcus abyssi (Q9UZR7)
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