Any feedback?
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, 5-5.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| 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 | Yersinia pestis |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified enzyme in complex with cofactors S-adenosyl-L-methionine and FAD or in complex with FAD alone, 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 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 | Yersinia pestis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Yersinia pestis | 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) | ? | - |
? |  |
| additional information | Yersinia pestis Kim | 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 | Yersinia pestis | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu | Yersinia pestis Kim | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | Yersinia pestis | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | Yersinia pestis Kim | - |
S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | Yersinia pestis | - |
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | Yersinia pestis Kim | - |
S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Yersinia pestis | Q8ZD36 | gene mnmC | - |
| Yersinia pestis Kim | Q8ZD36 | gene mnmC | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| 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 | Yersinia pestis |
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 Lmethionine-dependent methylation to yield methylaminomethyl uridine34 in the N-terminal domain active site | Yersinia pestis |
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) | Yersinia pestis | ? | - |
? | |
| 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) | Yersinia pestis Kim | ? | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu | - |
Yersinia pestis | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNAGlu | - |
Yersinia pestis Kim | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNAGlu + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | - |
Yersinia pestis | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl 2-thiouridine34 in tRNALys | - |
Yersinia pestis Kim | S-adenosyl-L-homocysteine + methylaminomethyl 2-thiouridine34 in tRNALys + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | - |
Yersinia pestis | S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
| S-adenosyl-L-methionine + carboxymethylaminomethyl uridine34 in tRNAArg | - |
Yersinia pestis Kim | S-adenosyl-L-homocysteine + methylaminomethyl uridine34 in tRNAArg + hydroxyacetate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | enzyme MnmC is monomeric in solution | Yersinia pestis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| MnmC | - |
Yersinia pestis |
| TrmC | - |
Yersinia pestis |
| YfcK | - |
Yersinia pestis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | required for oxidative cleavage of carboxymethyl group from cmnm5U34, FAD-binding site structure, overview | Yersinia pestis | |
| 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 | Yersinia pestis | |
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 | Yersinia pestis |
| 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 | Yersinia pestis |
| additional information | crystal structures of MnmC from two Gram negative bacteria reveal 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 structures of MnmC also reveal the detailed atomic interactions at the interdomain interface and provide spatial restraints relevant to the overall catalytic mechanism | Yersinia pestis |
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
