Literature summary for 2.1.1.207 extracted from

Benitez-Paez, A.; Villarroya, M.; Douthwaite, S.; Gabaldon, T.; Armengod, M.E.
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors (2010), RNA, 16, 2131-2143.

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Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
17726	-	2 * 17726, calulated from sequence	Escherichia coli
36000	-	gel filtration	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu	Escherichia coli	the enzyme methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeu(CmAA) and tRNALeu(cmnm5UmAA)	S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu	-	?
S-adenosyl-L-methionine + cytidine34 in tRNA	Escherichia coli	the enzyme methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeu(CmAA) and tRNALeu(cmnm5UmAA)	S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P0AGJ7	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-YibK protein	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu	the enzyme methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeu(CmAA) and tRNALeu(cmnm5UmAA)	Escherichia coli	S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu	-	?
S-adenosyl-L-methionine + cytidine34 in tRNA	the enzyme methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeu(CmAA) and tRNALeu(cmnm5UmAA)	Escherichia coli	S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA	-	?
S-adenosyl-L-methionine + cytidine34 in tRNA	the enzyme methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNALeu(CmAA) and tRNALeu(cmnm5UmAA). No methylation of fully synthetic in vitro transcrips of tRNA(CAA), lacking all natural modifications present in in vivo transcripts. The motifs in tRNALeu required for YibK recognition and catalysis include the N6-(isopentenyl)-2-methylthioadenosine (ms2i6A) at position 37 and a pyridine at position 34. It has a clear preference for adenosine at position 35	Escherichia coli	S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA	-	?

Subunits

Subunits	Comment	Organism
dimer	2 * 17726, calulated from sequence	Escherichia coli

Synonyms

Synonyms	Comment	Organism
methyltransferase yibK	-	Escherichia coli
Trml	-	Escherichia coli
tRNA (cytidine34/5-carboxymethylaminomethyluridine34'-O)-methyltransferase	-	Escherichia coli
tRNA methyltransferase L	-	Escherichia coli
YibK	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Escherichia coli

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Escherichia coli

General Information

General Information	Comment	Organism
malfunction	inactivation of yibK leads to loss of 2'-O-methylation at position 34 in both tRNALeu(CmAA) and tRNALeu(cmnm5UmAA). Loss of YibK methylation reduces the efficiency of codonwobble base interaction. Inactivation of yibK has no detectable effect on steady-state growth rate, although a distinct disadvantage is noted in multiple-round, mixed-population growth experiments, suggesting that the ability to recover from the stationary phase is impaired. Methylation is restored in vivo by complementing with a recombinant copy of yibK	Escherichia coli

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Release 2023.1 (January 2023)