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Information on EC 2.1.1.207 - tRNA (cytidine34-2'-O)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P0AGJ7

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     2 Transferases
         2.1 Transferring one-carbon groups
             2.1.1 Methyltransferases
                2.1.1.207 tRNA (cytidine34-2'-O)-methyltransferase
IUBMB Comments
The enzyme from Escherichia coli catalyses the 2'-O-methylation of cytidine or 5-carboxymethylaminomethyluridine at the wobble position at nucleotide 34 in tRNALeuCmAA and tRNALeucmnm5UmAA. The enzyme is selective for the two tRNALeu isoacceptors and only methylates these when they present the correct anticodon loop sequence and modification pattern. Specifically, YibK requires a pyrimidine nucleoside at position 34, it has a clear preference for an adenosine at position 35, and it fails to methylate without prior addition of the N6-(isopentenyl)-2-methylthioadenosine modification at position 37.
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This record set is specific for:
Escherichia coli
UNIPROT: P0AGJ7
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
+
5-carboxymethylaminomethyluridine34 in tRNALeu
=
+
5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu
Synonyms
trna (um34/cm34) methyltransferase, trna (cytidine/uridine-2'o)-ribose methyltransferase l, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C/U34 2-O-methyltransferase
-
methyltransferase yibK
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tRNA (cytidine/uridine-2'O)-ribose methyltransferase L
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tRNA (cytidine34/5-carboxymethylaminomethyluridine34'-O)-methyltransferase
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tRNA methyltransferase L
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tRNA (Um34/Cm34) methyltransferase
-
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2'-O)-methyltransferase
The enzyme from Escherichia coli catalyses the 2'-O-methylation of cytidine or 5-carboxymethylaminomethyluridine at the wobble position at nucleotide 34 in tRNALeuCmAA and tRNALeucmnm5UmAA. The enzyme is selective for the two tRNALeu isoacceptors and only methylates these when they present the correct anticodon loop sequence and modification pattern. Specifically, YibK requires a pyrimidine nucleoside at position 34, it has a clear preference for an adenosine at position 35, and it fails to methylate without prior addition of the N6-(isopentenyl)-2-methylthioadenosine modification at position 37.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu
S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNALeuCAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuCAA
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNALeuUAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuUAA
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNA
S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNALeuCAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuCAA
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + cytidine34 in tRNALeuUAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuUAA
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu
S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNALeu
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + cytidine34 in tRNALeuCAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuCAA
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + cytidine34 in tRNALeuUAA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine34 in tRNALeuUAA
show the reaction diagram
-
-
-
?
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNA
S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNA
show the reaction diagram
-
TrmL catalyzes the methyl transfer from SAM to the 2'-OH of the wobble nucleotide in tRNALeu cmnm5UmAA, which decodes codons UUA and UUG in the Phe/Leu mixed box, and tRNALeu CmAA, which reads the UUG codon included in the Leu family box
o.e. tRNALeucmnm5UmAA
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
S-adenosyl-L-methionine
additional information
-
no requirement of other protein cofactors
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
-
required
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00182 - 0.00537
cytidine34 in tRNALeuCAA
wild-type tRNALeuCAA and diverse mutants thereof, pH 7.5, 37°C
-
additional information
additional information
-
steady-state kinetic parameters of EcTrmL with modified tRNALeu substrates
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0073 - 0.2
cytidine34 in tRNALeuCAA
wild-type tRNALeuCAA and diverse mutants thereof, pH 7.5, 37°C
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme belongs to the SPOUT tRNA MTase superfamily
malfunction
metabolism
role of several tRNA modifications on rpoS or hfq expression: 2'-O-methylation of cytidine or uridine, at the wobble position (C/Um), 2-thiouridine at the wobble position (s2U), as well as isopentenyl adenosine 37(i6A37), overview
physiological function
evolution
metabolism
-
modifications at the wobble uridine, U34, of tRNAs reading two degenerate codons ending in purine are complex and result from the activity of two multi-enzyme pathways, the IscSeMnmA and MnmEG pathways, which independently work on positions 2 and 5 of the U34 pyrimidine ring, respectively, and from a third single-step pathway, controlled by TrmL, i.e. YibK, that modifies the 2'-hydroxyl group of the ribose. TrmL occurs as a late step in the maturation of the tRNALeu isoacceptors
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17726
2 * 17726, calulated from sequence
36000
gel filtration
17700
-
x * 17700, TrmL
19800
-
2 * 19800, SDS-PAGE and gel filtration, the overall structure of an EcTrmL monomer subunit is composed of six beta-strands and six alpha-helices, in the order beta1-alpha1-beta2-alpha2-alpha3-beta3-alpha4-beta4-beta5-alpha5-beta6-alpha6. EcTrmL dimer formation is essential for tRNA recognition. The residue Y142 is critical for maintaining the dimeric form of EcTrmL, which is consistent with its central position at the interface
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 17726, calulated from sequence
?
-
x * 17700, TrmL
homodimer
-
2 * 19800, SDS-PAGE and gel filtration, the overall structure of an EcTrmL monomer subunit is composed of six beta-strands and six alpha-helices, in the order beta1-alpha1-beta2-alpha2-alpha3-beta3-alpha4-beta4-beta5-alpha5-beta6-alpha6. EcTrmL dimer formation is essential for tRNA recognition. The residue Y142 is critical for maintaining the dimeric form of EcTrmL, which is consistent with its central position at the interface
additional information
TrmL-catalyzed 2'-O-methylation requires its homodimerization
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme TrmL in apoform and in complex with S-adenosyl-homocysteine, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement using the structure of Haemophilus influenzae Yibk, PDB ID 1J85 as starting search model, modeling
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K42E
-
site-directed mutagenesis, inactive mutant
K81E
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site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R104E
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
R129E
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site-directed mutagenesis, inactive mutant
R20E
-
site-directed mutagenesis, inactive mutant
R28E
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site-directed mutagenesis, the mutant shows slightly increased activity compared to the wild-type enzyme
R43E
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site-directed mutagenesis, inactive mutant
R45E
-
site-directed mutagenesis, inactive mutant
R46E
-
site-directed mutagenesis, inactive mutant
R59E
-
site-directed mutagenesis, inactive mutant
R64E
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
R74E
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Y142A
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site-directed mutagenesis, the mutant is a monomer in contrast to the wild-type enzyme. Mutant Y142A fails to form a complex with tRNA
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-YibK protein
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene rmL, recombinant expression of wild-type and mutant enzymes
gene trmL, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
RNA
16
2131-2143
2010
Escherichia coli (P0AGJ7)
Manually annotated by BRENDA team
Armengod, M.E.; Moukadiri, I.; Prado, S.; Ruiz-Partida, R.; Benitez-Paez, A.; Villarroya, M.; Lomas, R.; Garzon, M.J.; Martinez-Zamora, A.; Meseguer, S.; Navarro-Gonzalez, C.
Enzymology of tRNA modification in the bacterial MnmEG pathway
Biochimie
94
1510-1520
2012
Escherichia coli
Manually annotated by BRENDA team
Liu, R.J.; Zhou, M.; Fang, Z.P.; Wang, M.; Zhou, X.L.; Wang, E.D.
The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL
Nucleic Acids Res.
41
7828-7842
2013
Escherichia coli, Escherichia coli MT102
Manually annotated by BRENDA team
Zhou, M.; Long, T.; Fang, Z.P.; Zhou, X.L.; Liu, R.J.; Wang, E.D.
Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2-O-methyltransferase
RNA Biol.
12
900-911
2015
Escherichia coli (P0AGJ7)
Manually annotated by BRENDA team
Aubee, J.I.; Olu, M.; Thompson, K.M.
TrmL and TusA are necessary for rpoS and MiaA is required for hfq expression in Escherichia coli
Biomolecules
7
39
2017
Escherichia coli (P0AGJ7), Escherichia coli
Manually annotated by BRENDA team