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Literature summary for 2.1.1.229 extracted from
- Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC (2013), BMC Struct. Biol., 13, 5.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene mnmC, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3) | Escherichia coli |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified enzyme in complex with cofactors S-adenosyl-L-methionine and FAD, sitting drop vapor diffusion method, 21°C, 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 | Escherichia coli |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Escherichia coli | methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this posttranscriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the FAD-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine to yield methylaminomethyl uridine (mnm5U34) | ? | - |
? |  |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu | Escherichia coli | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | Escherichia coli | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | Escherichia coli | - |
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | - |
gene mnmC | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| 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 | Escherichia coli |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA = S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA | the C-terminal domain catalyzes the FAD-dependent oxidation of the Calpha-N bond in carboxymethylaminomethyl uridine34. The resulting imine intermediate is (presumably) non-enzymatically hydrolyzes to 5-aminomethyl uridine, followed by S-adenosyl-L-methionine-dependent methylation to yield methylaminomethyl uridine34 in the N-terminal domain active site | Escherichia coli |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the biosynthetic pathway responsible for this posttranscriptional modification, the bifunctional enzyme MnmC catalyzes the conversion of its hypermodified substrate carboxymethylaminomethyl uridine (cmnm5U34) to mnm5U34. MnmC catalyzes the FAD-dependent oxidative cleavage of carboxymethyl group from cmnm5U34 via an imine intermediate to generate aminomethyl uridine (nm5U34), which is subsequently methylated by S-adenosyl-L-methionine to yield methylaminomethyl uridine (mnm5U34) | Escherichia coli | ? | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu | - |
Escherichia coli | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | - |
Escherichia coli | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | - |
Escherichia coli | S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | enzyme MnmC is monomeric in solution | Escherichia coli |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| MnmC | - |
Escherichia coli |
| TrmC | - |
Escherichia coli |
| YfcK | - |
Escherichia coli |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | required for oxidative cleavage of carboxymethyl group from cmnm5U34, FAD-binding site structure, overview | Escherichia coli | |
| S-adenosyl-L-methionine | dependent on, the N-terminal MnmC2 domain is composed of residues 1-245 and contains the SAM binding site. The binding pocket is composed of mostly hydrophobic residues, except for Glu101 and Asp178 | Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | comparison of the MnmC2 active sites between Escherichia coli MnmC and Yersinia pestis MnmC, overview. Structural comparison with MnmC2 of Aquifex aeolicus | Escherichia coli |
| metabolism | MnmC (formally known as YfcK or TrmC) is a bifunctional enzyme responsible for the final two steps of biosynthetic pathway of mnm5s2U in tRNAGlu and tRNALys, and mnm5U in tRNAArg | Escherichia coli |
| additional information | crystal structure of MnmC from the Gram negative bacterium reveals the overall architecture of the enzyme and the relative disposition of the two independent catalytic domains: a Rossmann-fold domain containing the S-adenosyl-L-methionine binding site and an FAD containing domain structurally homologous to glycine oxidase from Bacillus subtilis. The structure of MnmC also reveals the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism | Escherichia coli |
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