Bifunctional tRNA modification enzyme MnmC from Escherichia coli
Classification:
TRANSFERASE, OXIDOREDUCTASE
Technique:
X-Ray Diffraction
Resolution:
3.0
R value free:
0.251
R value observed:
0.205
R value work:
0.204
Abstract of the PDB Structure's related Publication:
Post-transcriptional modifications of bases within the transfer RNAs (tRNA) anticodon significantly affect the decoding system. In bacteria and eukaryotes, uridines at the wobble position (U34) of some tRNAs are modified to 5-methyluridine derivatives (xm⁵U). These xm⁵U34-containing tRNAs read codons ending with A or G, whereas tRNAs with the unmodified U34 are able to read all four synonymous codons of a family box. In Escherichia coli (E.coli), the bifunctional enzyme MnmC catalyzes the two consecutive reactions that convert 5-carboxymethylaminomethyl uridine (cmnm⁵U) to 5-methylaminomethyl uridine (mnm⁵U). The C-terminal domain of MnmC (MnmC1) is responsible for the flavin adenine dinucleotide (FAD)-dependent deacetylation of cmnm⁵U to 5-aminomethyl uridine (nm⁵U), whereas the N-terminal domain (MnmC2) catalyzes the subsequent S-adenosyl-L-methionine-dependent methylation of nm⁵U, leading to the final product, mnm⁵U34. Here, we determined the crystal structure of E.coli MnmC containing FAD, at 3.0 Å resolution. The structure of the MnmC1 domain can be classified in the FAD-dependent glutathione reductase 2 structural family, including the glycine oxidase ThiO, whereas the MnmC2 domain adopts the canonical class I methyltransferase fold. A structural comparison with ThiO revealed the residues that may be involved in cmnm⁵U recognition, supporting previous mutational analyses. The catalytic sites of the two reactions are both surrounded by conserved basic residues for possible anticodon binding, and are located far away from each other, on opposite sides of the protein. These results suggest that, although the MnmC1 and MnmC2 domains are physically linked, they could catalyze the two consecutive reactions in a rather independent manner.
In E.coli (and many other bacteria) it is a bifunctional enzyme, composed of two domains that catalyze two successive reactions at the uridine wobble position 34 in tRNA: first a deacetylation reaction of cmnm5U into nm5U, then methylation of the amine group of nm5U to form mnm5U. In other organisms they may be unlinked (separate proteins), then identified as MnmC (former MnmC1) for the deacetylase and MnmD (former MnmC2) for the methyltransferase. In certain bacteria, the catalytic domain for the deacetylation reaction is absent in their genome and only the gene coding for MnmD is present. In other bacteria, MnmC and MnmD are both present. In E. coli MnmCD the two domains act independently. For tRNALeucmnm5Um the activity of methyltransferase domain was observed only in vitro (
Bujnicki et al. 2004).
Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U.
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM
The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species.
Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U.
Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli.
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC.
The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species.