Information on EC 2.1.1.229 - tRNA (carboxymethyluridine34-5-O)-methyltransferase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
2.1.1.229
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RECOMMENDED NAME
GeneOntology No.
tRNA (carboxymethyluridine34-5-O)-methyltransferase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA = S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
tRNA methylation (yeast)
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (carboxymethyluridine34-5-O)-methyltransferase
The enzyme catalyses the posttranslational modification of uridine residues at the wobble position 34 of the anticodon loop of tRNA.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SwissProt
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
gene mnmC
UniProt
Manually annotated by BRENDA team
gene mnmC
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
additional information
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 + carboxymethyl-2-thiouridine34 in tRNA
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)-2-thiouridine34 in tRNA
show the reaction diagram
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Trm9-Trm112, subunit Trm112 is required for the activity, but role of Sc Trm112 in the complex is not for catalysis
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-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu
show the reaction diagram
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-
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?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys
show the reaction diagram
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-
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-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg
show the reaction diagram
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-
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-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
show the reaction diagram
S-adenosyl-L-methionine + carboxymethyluridine34 in tRNAArg3
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
show the reaction diagram
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-
-
?
S-adenosyl-L-methionine + carboxymethyluridine34 in tRNAGlU
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
show the reaction diagram
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-
-
?
S-adenosyl-S-carboxymethyl-L-homocysteine + 5-methoxyuridine34 in tRNA
S-adenosyl-L-methionine + uridine 5-oxyacetic acid in tRNA
show the reaction diagram
proposed modification pathway of 5-oxyuridine derivatives, overview
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-
?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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 + carboxymethyl-2-thiouridine34 in tRNA
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)-2-thiouridine34 in tRNA
show the reaction diagram
-
Trm9-Trm112, subunit Trm112 is required for the activity, but role of Sc Trm112 in the complex is not for catalysis
-
-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate
show the reaction diagram
S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA
S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
S-adenosyl-S-carboxymethyl-L-homocysteine
i.e. [(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(carboxymethyl)sulfanium, the enzyme contains a cofactor, S-adenosyl-S-carboxymethyl-L-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other S-adenosyl-L-methionine-containing enzymes. The active site contains one molecule cofactor S-adenosyl-S-carboxymethyl-L-homocysteine per monomer, and not S-adenosyl-L-methionine
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
TRM112
interaction of ALKBH8 with a small accessory protein, TRM112, is required to form a functional tRNA methyltransferase
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Trm112 p
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the presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro
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Trm112p
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when produced in Escherichia coli, Trm112p forms a complex with Trm9p, which renders the latter soluble. This recombinant complex catalyzes the formation of mcm5U34 (5-methoxycarbonylmethyluridine) on tRNA in vitro but not mcm5s2U34 (5-methoxycarbonylmethyl-2-thiouridine)
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 x 52500, gel filtration, mass spectrometry, and crystal structure analysis, 2 * 55600, about, sequence calculation. There are two molecules of CmoA present in the asymmetric unit, both molecules of CmoA contain the novel derivative S-adenosyl-S-carboxymethyl-L-homocysteine, the two molecules adopt the same conformation
heterodimer
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the enzyme is formed by catalytic subunit Trm9 and regulatory subunit Trm112
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified enzyme in complex with cofactors S-adenosyl-L-methionine and FAD, sitting drop vapor diffusion method, 21C, by mixing 0.001 ml of 10 mg/ml protein with 0.001 ml of reservoir solution containing 1.8 M tri-ammonium citrate, pH 7.0 and 0.5% ethyl acetate, X-ray diffraction structure determination and analysis at 2.3 A resolution
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purified MnmC containing FAD, sitting drop method, the optimal reservoir solution contains 100 mM Bis-Tris, pH 5.5, containing 25% w/v PEG3350, 250 mM ammonium sulfate, and 10 mM hexamine cobalt(III) chloride, 5 days, X-ray diffraction structure determination and analysis at 3.0 A resolution
purified recombinant detagged enzyme, sitting drop vapour diffusion method, mixing of 100 nl of 20 mg/ml protein in 200 mM NaCl, and 20 mM Tris, pH 7.5, with 100 nl of precipitation solution containing 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M MOPS/HEPES-Na, pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% w/v MPD, 5 h, X-ray diffraction structure determination and analysis at 1.73 A resolution, molecular replacement using the structure of Haemophilus influenzae YecO, PDB ID 1im8, chain B
purified enzyme in complex with cofactors S-adenosyl-L-methionine and FAD or in complex with FAD alone, sitting drop vapor diffusion method, 21C, by mixing 0.001 ml of 10 mg/ml protein with 0.001 ml of reservoir solution containing 0.1 M HEPES, pH 7.0, and 30% v/v Jeffamine ED-2001 reagent, X-ray diffraction structure determination and analysis at 2.3 A resolution
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
co-purification of His-tagged Trm9p with untagged Trm112p as a complex from Escherichia coli strain BL21(DE3)pLysS by nickel affinity chromatography
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recombinant His-tagged enzyme from Escherichia coli strain Rosetta pLysS (DE3) by nickel affinity chromatography and gel filtration, followed by cleavage of the N-terminal His6-tag with rhinovirus 3C protease and another step of nickel affinity chromatography to remove the tag
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag cleavage with thrombin , and again nickel adffinity chromatography for tag removal, followed by gel filtration
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recombinant N-terminally His6-tagged wild-type and selenomethionine-labeled enzyme from Escherichia coli strains by nickel affinity chromatography, tag cleavage with enterokinase, and again nickel adffinity chromatography for tag removal, followed by gel filtration
recombinant wild-type and selenomethinone-labeled enzymes from Escherichia coli by ultracentrifugation, anion exchange and hydrophobic interaction chromatography, another step of anion exchange chromatography and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
co-expression of His-tagged Trm9p with untagged Trm112p in Escherichia coli strain BL21(DE3)pLysS, Trm9p/Trm112p complex formation
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expression in Escherichia coli
expression of GST-Trm9 fusion protein in Escherichia coli DH5alpha cells
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gene cmoA, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli strain Rosetta pLysS (DE3)
gene JW5380, expression of wild-type and selenomethinone-labeled MnmC in Escherichia coli strains Rosetta2(DE3) and B834(DE3), respectively
gene mnmC, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
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gene mnmC, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3), expression of selenomethionine-labeled enzyme in Escherichia coli strain B834
the FLAG-tagged-ABH8 coding region is cloned into the pBABEpuro or pBABEhygro retroviral vector. HeLa S3 cells are infected with retrovirus
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
DNA-damaging agents induce ABH8 expression in an ATM(central DNA damage kinase)-dependent manner
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R618A
the mutation abolishes the activity of MnmC
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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transurethral injection of ALKBH8 small interfering RNA (siRNA) offers promise as a new therapeutic strategy for bladder cancer