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Information on EC 2.1.1.35 - tRNA (uracil54-C5)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P23003
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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: Escherichia coli
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
m5U-methyltransferase
-
-
-
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methyltransferase, transfer ribonucleate uracil 5-
-
-
-
-
ribothymidyl synthase
-
-
-
-
rTase
-
-
-
-
RUMT
-
-
-
-
transfer RNA uracil 5-methyltransferase
-
-
-
-
transfer RNA uracil methylase
-
-
-
-
tRNA uracil 5-methyltransferase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
catalytic mechanism
-
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
steric course of methyl transfer
-
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
single SN2 displacement mechanism
-
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
detailed chemical and enzymatic mechanism
-
S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
kinetic, sequential mechanism
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
methyl group transfer
methyl group transfer
-
-
-
-
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
-
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 + 16S rRNA
S-adenosyl-L-homocysteine + 16S rRNA containing thymine
S-adenosyl-L-methionine + DNA analog of the T-stem/loop domain of yeast tRNAPhe
S-adenosyl-L-homocysteine + DNA analog of the T-stem/loop domain of yeast tRNAPhe containing thymine
-
DNA analog of the T-stem/loop domain of yeast tRNAPhe composed of d(A,U,G,C) is also a substrate, slow methylation of tDNAPheT
-
?
S-adenosyl-L-methionine + tRNA containing uridine at position 54
S-adenosyl-L-homocysteine + tRNA containing ribothymidine at position 54
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in 11mer of the T-arm of E. coli tRNA1-Val
S-adenosyl-L-homocysteine + 5-methyluracil54 in 11mer of the T-arm of E. coli tRNA1-Val
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in 17mer of the T-arm of E. coli tRNA1-Val
S-adenosyl-L-homocysteine + 5-methyluracil54 in 17mer of the T-arm of E. coli tRNA1-Val
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in methyl deficient tRNA from E. coli
?
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in unmodified E. coli tRNA1-Val
S-adenosyl-L-homocysteine + 5-methyluracil54 in unmodified E. coli tRNA1-Val
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in unmodified T-stem/loop domain of yeast tRNA-Phe
S-adenosyl-L-homocysteine + 5-methyluracil54 in unmodified T-stem/loop domain of yeast tRNA-Phe
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in unmodified yeast tRNA-Phe TPsiC-stem and loop heptadecamer
S-adenosyl-L-homocysteine + 5-methyluracil54 in unmodified yeast tRNA-Phe TPsiC-stem and loop heptadecamer
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in wheat germ tRNA1-Gly
S-adenosyl-L-homocysteine + 5-methyluracil54 in in wheat germ tRNA1-Gly
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in yeast tRNA-Phe
S-adenosyl-L-homocysteine + 5-methyluracil54 in yeast tRNA-Phe
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in yeast tRNA1-Phe
S-adenosyl-L-homocysteine + 5-methyluracil54 in yeast tRNA1-Phe
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
S-adenosyl-L-methionine + 16S rRNA
S-adenosyl-L-homocysteine + 16S rRNA containing thymine
-
methyl group acceptor: E. coli 16S rRNA, site of methylation is U788 which is within a 9-base loop of a predicted stem-loop structure, mechanism is proposed to involve formation of a covalent, reversible Michael adduct with the target U788, poor substrate: methylation of 16S rRNA 40fold slower than of tRNAPhe
in vitro product m5U is not normally found in wild-type 16S rRNA, U788 is not highly methylated in vivo, 1 mol m5U per mol of 16S rRNA
?
S-adenosyl-L-methionine + 16S rRNA
S-adenosyl-L-homocysteine + 16S rRNA containing thymine
-
unmodified E. coli 16S rRNA can be methylated at U788
-
?
S-adenosyl-L-methionine + uracil54 in yeast tRNA1-Phe
S-adenosyl-L-homocysteine + 5-methyluracil54 in yeast tRNA1-Phe
-
-
-
-
?
S-adenosyl-L-methionine + uracil54 in yeast tRNA1-Phe
S-adenosyl-L-homocysteine + 5-methyluracil54 in yeast tRNA1-Phe
-
-
-
-
r
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
-
methylates 5-carbon of U in position 54 of tRNA, product is ribothymidine, which is invariant in the TPsiC loop
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: methyl-deficient tRNA from E. coli
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: methyl-deficient tRNA from E. coli
-
ir
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: methyl-deficient tRNA from E. coli
one ribothymidine per tRNA molecule, always at the 23rd nucleotide from the 3 end
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: methyl-deficient tRNA from E. coli
methylates 5-carbon of U in position 54 of tRNA, product is ribothymidine, which is invariant in the TPsiC loop
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
highly specific for tRNA and S-adenosyl-L-methionine, cannot be replaced by methionine plus ATP, formaldehyde plus tetrahydrofolic acid, methylcobalamin and methyltetrahydrofolic acid
-
ir
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA recognition reside in the 3-dimensional structure of the 7-member T-loop rather than in its primary structure, base composition of the T-stem is also unimportant, only U54 and C56 are essential for activity, tRNA binding causes a conformational change of tRNA to expose the modification site in the T-arm
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
5-methylation of U in the TPsiC-loop
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
enzyme transfers methyl group to uridine in position 54 of the TPsi-loop of all E. coli tRNA species, requires the TPsi-arm and, most specifically, the bases U54-U55-C56-Pu57-A58 for tRNA recognition
formation of 5-methyluridine
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
S-adenosyl-L-methionine/S-adenosyl-L-homocysteine binding site, terminal NH2-group of the amino acid moiety is nessecary for activity
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
extend of methylation is directly proportional to the amount of tRNA added, 0.5% of nucleotide residues are methylated
-
ir
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: thymine-deficient tRNA from E. coli trmA-mutant
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: methyl-deficient and T-deficient E. coli tRNA, enzyme recognizes and methylates TSL: a minimal unmodified yeast tRNAPhe TPsiC-stem and loop heptadecamer, composed of a 5 bp stem and seven-membered loop, recognition determinants are contained within the sequence, modification and secondary structure of TSL, enzyme is sensitive to conformational perturbations at or adjacent to the methylation site, positions 54 and 55
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: small RNA oligomers corresponding to the T-arm of tRNA, 17-oligomer
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: E. coli tRNA1Val, 17-oligomer and 11-oligomer of the T-arm of tRNA1Val, essential sequence for tRNA binding: within the T-arm, composed of 7-base T-loop and 5-base pair stem, includes position 52 of T-stem, the T-loop and extends to the 3'-acceptor end, methylation site at U54
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNAs from wheat germ are the best substrates
formation of 5-methyluridine
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
substrate consensus sequence for the T-arm of tRNA consists of a 2-5 base-pair stem and a 7-base loop
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
substrate consensus sequence for the T-arm of tRNA consists of a 2-5 base-pair stem and a 7-base loop
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: tRNA from Micrococcus lysodeikticus
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: m5U-deficient tRNA from E. coli GB1-5-39
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: m5U-deficient tRNA from E. coli GB1-5-39
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: m5U-deficient tRNA from E. coli GB1-5-39
methylates 5-carbon of U in position 54 of tRNA, product is ribothymidine, which is invariant in the TPsiC loop
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: unmodified yeast tRNAPhe
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: unmodified yeast tRNAPhe
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: unmodified yeast tRNAPhe
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: unmodified yeast tRNAPhe
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: unmodified T-stem/loop domain of yeast tRNAPhe, methyl-deficient tRNA from E. coli C6 rel met- cys-, riboT-deficient tRNA from E. coli TrmA- is a specific substrate for U54 methylation, enzyme recognizes almost all tRNAs
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: tRNA from E. coli
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: tRNA from E. coli
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: tRNA from E. coli
formation of 5-methyluridine
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: E. coli tRNA1Val, 17-mer analog of the T-arm from tRNA1Val
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
high substrate specificity, methyl group acceptors: wheat germ tRNA1Gly, tRNA2Gly, E. coli tRNA1Ala
formation of 5-methyluridine
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: a variety of tRNA substrates including prokaryotic, eukaryotic, mitochondrial and chloroplastic tRNAs, wheat germ tRNA1Gly, bovine liver tRNAVal, Dictyostelium discoideum vegetative stage mitochondrial tRNA and rabbit liver tRNA, methylates E. coli tRNAs at a specific U residue 23 nucleotides from the 3 end
formation of 5-methyluridine
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptors: E. coli tRNAPhe, tRNAVal
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA recognition
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA recognition
methylates 5-carbon of U in position 54 of tRNA, product is ribothymidine, which is invariant in the TPsiC loop
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
enzyme is normally tightly associated with the tRNA
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA and S-adenosyl-L-methionine have separate and independent binding sites
one ribothymidine per tRNA molecule, always at the 23rd nucleotide from the 3 end
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methylation of U54
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methylates U54 in the TPsiC-loop of tRNA
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methylates U54 in the TPsiC-loop of tRNA
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methylates U54 in the TPsiC-loop of tRNA
formation of 5-methyluridine in position 54 of tRNA, in the TPsiC sequence in loop IV
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
methyl group acceptor: thymine-deficient tRNA from E. coli
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
in vivo present both as 42 kDa polypeptide and as covalent TrmA/RNA complex, to equal amounts, both with methylating activity, in vivo the m5U54 modification confers a small selective growth advantage, two different catalytic activities: synthesis of m5U54 and an unknown essential function, may be associated with binding RNA, either during a maturation process of the rRNA and/or tRNA or as a regulatory device during the assembly and maturation of the translational apparatus such as an RNA chaperone
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
specific reaction in maturation of tRNA
ribothymidine is the most common methylated nucleoside found in tRNA, it occurs in all tRNAs of the organism
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
enzyme-tRNA complexes may exist as dihydrouridine intermediates and may serve as reservoirs of RUMT-tRNA complexes primed for methylation
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
involved in biosynthesis of all tRNA chains, association of enzyme to tRNA may be of regulatory significance
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
specific inhibition of enzyme by ethionine in vivo
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
primary function of nucleoside modification within the tRNA anticodon loop is to negate potential canonical base pairs that would close the loop and, thereby, hinder codon binding
-
?
additional information
additional information
-
-
not as methyl group acceptors: methyl-deficient DNA from E. coli, polyadenylic acid, polycytidylic acid, polyuridylic acid, polyinosinic acid, copolymers of adenylic acid and uridylic acid and of guanylic acid and cytidylic acid, tobacco mosaic viral RNA, turnip yellow mosaic viral RNA, RNA from bacteriophage f2, CMP, AMP, UMP, GMP, rRNA
-
-
?
additional information
additional information
-
-
enzyme also catalyzes exchange of tritium of [3H]-Ura-16S rRNA and protons of water
-
-
?
additional information
additional information
-
-
detailed mechanism, Cys-324 is the nucleophilic catalyst of enzyme, involves SN2 attack of C5 of U54 on the methyl group of AdoMet
-
-
?
additional information
additional information
-
-
poor acceptors: tRNAs from spinach chloroplasts, Dictyostelium discoideum vegetative stage, Bacillus subtilis and Anacystis nidulans, unfractionated E. coli tRNA
-
-
?
additional information
additional information
-
-
up to 50% of enzyme is covalently bound to various tRNA species, including several tRNAs at the 3 end of 16S rRNA
-
-
?
additional information
additional information
-
-
enzyme is present as 42 kDa native protein or as 2 different covalent TrmA/RNA complexes, with TrmA as a 54 kDa and a 62 kDa polypeptide, respectively, RNA is a subset of undermodified tRNA species as well as the 3 terminus of 16S rRNA, RNA does not affect enzyme activity
-
-
?
additional information
additional information
-
-
enzyme is present as 42 kDa native protein or as 48-57 kDa RNA-protein complex, RNA is not essential, but may increase enzyme activity
-
-
?
additional information
additional information
-
-
enzyme also catalyzes an S-adenosyl-L-methionine-independent exchange reaction between [5-3H]-Urd-labeled substrate tRNA and protons of water at 1% of the normal methylation reaction rate, mechanism
-
-
?
additional information
additional information
-
-
enzyme also catalyzes an S-adenosyl-L-methionine-independent exchange reaction between [5-3H]-Urd-labeled substrate tRNA and protons of water at 1% of the normal methylation reaction rate, mechanism
-
-
?
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
-
-
-
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
in vivo present both as 42 kDa polypeptide and as covalent TrmA/RNA complex, to equal amounts, both with methylating activity, in vivo the m5U54 modification confers a small selective growth advantage, two different catalytic activities: synthesis of m5U54 and an unknown essential function, may be associated with binding RNA, either during a maturation process of the rRNA and/or tRNA or as a regulatory device during the assembly and maturation of the translational apparatus such as an RNA chaperone
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
specific reaction in maturation of tRNA
ribothymidine is the most common methylated nucleoside found in tRNA, it occurs in all tRNAs of the organism
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
tRNA modifying enzyme
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
enzyme-tRNA complexes may exist as dihydrouridine intermediates and may serve as reservoirs of RUMT-tRNA complexes primed for methylation
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
involved in biosynthesis of all tRNA chains, association of enzyme to tRNA may be of regulatory significance
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
specific inhibition of enzyme by ethionine in vivo
-
?
S-adenosyl-L-methionine + uridine54 in tRNA
S-adenosyl-L-homocysteine + 5-methyluridine54 in tRNA
-
primary function of nucleoside modification within the tRNA anticodon loop is to negate potential canonical base pairs that would close the loop and, thereby, hinder codon binding
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
DNA analog of the T-stem/loop domain
-
DNA analog of the T-stem/loop domain of yeast tRNAPhe composed of d(A,U,G,C) inhibits the methylation of unfractionated methyl-deficient E. coli tRNA, significant inhibition when the concentration of tDNAPheT is twice that of the tRNA
-
L-ethionine
-
selective inhibitor of uracil tRNA methylase, non-competitive to S-adenosyl-L-methionine
mature tRNA
-
weak, competitive inhibitor to methyl-deficient tRNA, non-competitive to S-adenosyl-L-methionine
NO2Ura-tRNA
-
potent mechanism-based inhibitor, competitive with respect to tRNA, can be reversed by dilution into a large excess of tRNA substrate, forms a reversible covalent complex in which Cys-324 of RUMT is linked to the 6-position of NO2-Ura 54 in NO2-Ura-tRNA, mechanism
-
5-Fluorouracil substituted tRNA
-
first-order inactivation in the presence of S-adenosyl-L-methionine, potent mechanism-based irreversible inhibition, formation of a stable covalent complex containing enzyme, FUra-tRNA and the methyl group of AdoMet
-
5-Fluorouracil substituted tRNA
-
forms inhibitory stable methylated covalent complex with RUMT
-
p-chloromercuribenzoate
-
at 2.5 mM, complete inhibition, completely reversed by addition of 5 mM dithiothreitol
S-adenosyl-L-homocysteine
-
product inhibition, competitive to S-adenosyl-L-methionine
S-adenosyl-L-homocysteine
-
product inhibition, inhibits both methylation and H-exchange reaction
S-adenosyl-L-homocysteine
-
product inhibition, reversed by S-adenosylmethionine
S-adenosyl-L-homocysteine
-
at 0.002 mM 50% inhibition, E. coli MRE 600
structural analogues of S-adenosyl-L-homocysteine
-
inhibition competitive to S-adenosyl-L-methionine
-
structural analogues of S-adenosyl-L-homocysteine
-
nitrogen analogue of S-adenosyl-L-methionine AdoMDB inhibits at high concentrations methylation but increases H-exchange reaction
-
additional information
-
not inhibited by alanine, valine, ethionine sulfoxide
-
additional information
-
not inhibited by spermine, adenosine, L-homocysteine, snake venom phosphodiesterase
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
spermidine
-
slight activation at 20 mM in presence of 50 mM ammonium acetate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0156
uracil54 in unmodified yeast tRNA-Phe TPsiC-stem and loop heptadecamer
-
-
-
additional information
additional information
-
values for several mutants of yeast tRNAPhe
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
values for several mutants of yeast tRNAPhe
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
42000
54000
62000
42000
-
1 * 42000, native protein, additional bands at 32, 41, 48-57 kDa, polypeptides ranging over 48-57 kDa are dependent on the gel system used and refer to the RNA-enzyme complex, SDS-PAGE
54000
-
RNA-enzyme complex: RNA component associated with the 41/42 kDa polypeptide, PAGE
62000
-
during the synthesis of m5U54 a covalent 62 kDa TrmA-tRNA intermediate is formed, determined by SDS-PAGE and immunoblotting
62000
-
x * 54000, first TrmA/RNA-complex, x * 62000, second TrmA/RNA-complex, x * 42000, native enzyme form, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
?
-
x * 54000, first TrmA/RNA-complex, x * 62000, second TrmA/RNA-complex, x * 42000, native enzyme form, SDS-PAGE
monomer
-
1 * 42000, native protein, additional bands at 32, 41, 48-57 kDa, polypeptides ranging over 48-57 kDa are dependent on the gel system used and refer to the RNA-enzyme complex, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the structure of Escherichia coli E358Q 5-methyluridine 54 tRNA methyltransferase, in a covalent complex with a 19 nt T arm analog, is solved to 2.4 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E358Q
mutation of the catalytic base Glu-358 to Gln arrests catalysis and allows isolation of the covalent protein-RNA complex for crystallization
C324A
-
level of total TrmA-associated peptide 41%, amount of m5U in total tRNA 4%, relative to the levels found in the wild-type
D299A
-
level of total TrmA-associated peptide 63%, amount of m5U in total tRNA 1%, relative to the levels found in the wild-type
E358K
-
level of total TrmA-associated peptide 59%, amount of m5U in total tRNA 9%, relative to the levels found in the wild-type
F188A
-
level of total TrmA-associated peptide 84%, amount of m5U in total tRNA 22%, relative to the levels found in the wild-type
G220D
-
level of total TrmA-associated peptide 76%, amount of m5U in total tRNA 2%, relative to the levels found in the wild-type
G360D
-
level of total TrmA-associated peptide 53%, amount of m5U in total tRNA 1%, relative to the levels found in the wild-type
Q190A
-
level of total TrmA-associated peptide 77%, amount of m5U in total tRNA 14%, relative to the levels found in the wild-type
R302A
-
level of total TrmA-associated peptide 82%, amount of m5U in total tRNA 87%, relative to the levels found in the wild-type
W132C
-
level of total TrmA-associated peptide 102%, amount of m5U in total tRNA 34%, relative to the levels found in the wild-type
W202C
-
level of total TrmA-associated peptide 1%, amount of m5U in total tRNA 15%, relative to the levels found in the wild-type
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, crude extract, 10 mM potassium phosphate, pH 7, 1 mM EDTA, 0.1 mM dithiothreitol, 10% v/v ethylene glycol, 0.02% sodium azide, 7 days, 10% loss of activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the His6 tag protein is purified using a Talon column, the tag is cleaved by thrombin, thrombin is removed by passage over a benzamidine column
polyethyleneimine precipitation, phosphocellulose and affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
hybrid plasmid carrying trmA gene encoding enzyme is used to amplify enzyme production, trmA gene is sequenced
-
the plasmids pGP100, pDM4, pKD4 and pKD46 are used for the construction of the mutants
-
trmA gene encodes enzyme, gene is essential for the organism
-
trmA gene encoding for RUMT is cloned into a pET vector and transformed into Escherichia coli BL21 (DE3) cells, extremely high-level expression system
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
-
enzyme is used for detecting tRNA-like moieties in viral RNA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hurwitz, J.; Gold, M.; Anders, M.
The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. III. Purification of soluble ribonucleic acid-methylating enzymes
J. Biol. Chem.
239
3462-3473
1964
Escherichia coli
Hurwitz, J.; Gold, M.; Anders, M.
The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. IV. The properties of the soluble ribonucleic acid-methylating enzymes
J. Biol. Chem.
239
3474-3482
1964
Escherichia coli
Shugart, L.; Chastain, B.
Escherichia coli tRNA (uracil-5-)-methyltransferase: Inhibition by analogues of adenosylhomocysteine
Enzyme
24
353-357
1979
Escherichia coli
Greenberg, R.; Dudock, B.
Isolation and characterization of m5U-methyltransferase from Escherichia coli
J. Biol. Chem.
255
8296-8302
1980
Escherichia coli, Escherichia coli MRE 600, Escherichia coli SN01
Greenberg, R.; Dudock, B.
Bacterial tRNA methyltransferases
Methods Enzymol.
59
190-203
1979
Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Escherichia coli MRE 600
Gustafsson, C.; Bjrk, G.R.
The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3-end fragment of 16S rRNA
J. Biol. Chem.
268
1326-1331
1993
Escherichia coli, Escherichia coli 1100
Shugart, L.
Kinetic studies of Escherichia coli transfer RNA (uracil-5-)-methyltransferase
Biochemistry
17
1068-1072
1978
Escherichia coli, Escherichia coli K12MO7
Santi, D.V.; Hardy, L.W.
Catalytic mechanism and inhibition of tRNA (uracil-5-)methyltransferase: Evidence for covalent catalysis
Biochemistry
26
8599-8606
1987
Escherichia coli, Escherichia coli GB-1-5-39 / pTN102
Gu, X.; Santi, D.V.
The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferase
Biochemistry
30
2999-3002
1991
Escherichia coli
Ny, T.; Lindstrm, P.H.R.; Hagervall, T.G.; Bjrk, G.R.
Purification of transfer RNA (m5U54)-methyltransferase from Escherichia coli. Association with RNA
Eur. J. Biochem.
177
467-475
1988
Escherichia coli, Escherichia coli C600 / pTN106
Kealey, J.T.; Lee, S.; Floss, H.G.; Santi, D.V.
Stereochemistry of methyl transfer catalyzed by tRNA (m5U54)-methyltransferase--evidence for a single displacement mechanism
Nucleic Acids Res.
19
6465-6468
1991
Escherichia coli
Tscherne, J.S.; Wainfan, E.
Selective inhibition of uracil tRNA methylases of E. coli by ethionine
Nucleic Acids Res.
5
451-461
1978
Escherichia coli
Kealey, J.T.; Gu, X.; Santi, D.V.
Enzymatic mechanism of tRNA (m5U54)methyltransferase
Biochimie
76
1133-1142
1994
Escherichia coli
Kealey, J.T.; Santi, D.V.
High-level expression and rapid purification of tRNA (m5U54)-methyltransferase
Protein Expr. Purif.
5
149-152
1994
Escherichia coli, Escherichia coli GB-1-5-39 / pTN102
Gu, X.; Matsuda, A.; Ivanetich, K.M.; Santi, D.V.
Interaction of tRNA (uracil-5-)-methyltransferase with NO2Ura-tRNA
Nucleic Acids Res.
24
1059-1064
1996
Escherichia coli
Kealey, J.T.; Santi, D.V.
Stereochemistry of tRNA(m5U54)-methyltransferase catalysis: 19F NMR spectroscopy of an enzyme-FUraRNA covalent complex
Biochemistry
34
2441-2446
1995
Escherichia coli
Gu, X.; Ofengand, J.; Santi, D.V.
In vitro methylation of Escherichia coli 16S rRNA by tRNA (m5U54)-methyltransferase
Biochemistry
33
2255-2261
1994
Escherichia coli
Guenther, R.H.; Bakal, R.S.; Forrest, B.; Chen, Y.; Sengupta, R.; Nawrot, B.; Sochacka, E.; Jankowska, J.; Kraszewski, A.; Malkiewicz, A.; Agris, P.F.
Aminoacyl-tRNA synthetase and U54 methyltransferase recognize conformations of the yeast tRNAPhe anticodon and T stem/loop domain
Biochimie
76
1143-1151
1994
Escherichia coli
Sengupta, R.; Vainauskas, S.; Yarian, C.; Sochacka, E.; Malkiewicz, A.; Guenther, R.H.; Koshlap, K.M.; Agris, P.F.
Modified constructs of the tRNA TPsiC domain to probe substrate conformational requirements of m1A58 and m5U54 tRNA methyltransferases
Nucleic Acids Res.
28
1374-1380
2000
Escherichia coli, Escherichia coli GRB822
Gu, X.; Ivanetich, K.M.; Santi, D.V.
Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific
Biochemistry
35
11652-11659
1996
Escherichia coli
Urbonavicius, J.; Jaeger, G.; Bjoerk, G.R.
Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity
Nucleic Acids Res.
35
3297-3305
2007
Escherichia coli
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