8H0S

Crystal structure of MnmM from B. subtilis complexed with Gln-TTG anti-codon stem loop and SAM (2.90 A)

Summary for 8H0S

• Entry DOI: 10.2210/pdb8h0s/pdb
• Descriptor: Putative rRNA methylase YtqB, RNA (5'-R(*AP*CP*GP*GP*AP*CP*UP*UP*UP*GP*AP*CP*UP*CP*CP*GP*U)-3'), S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: methyltransferase, trna post-transcriptional modification, mnmc mnm5(s2)u, transferase-rna complex, transferase/rna
• Biological source: Bacillus subtilis subsp. subtilis str. 168; More
• Total number of polymer chains: 6
• Total formula weight: 101367.21

Authors

Kim, J.,Lee, J.,Cho, G. (deposition date: 2022-09-30, release date: 2023-01-25, Last modification date: 2023-10-25)

Primary citation

Cho, G.,Lee, J.,Kim, J.
Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification.
Nucleic Acids Res., 51:1971-1983, 2023

PubMed Abstract: The uridine at the 34th position of tRNA, which is able to base pair with the 3'-end codon on mRNA, is usually modified to influence many aspects of decoding properties during translation. Derivatives of 5-methyluridine (xm5U), which include methylaminomethyl (mnm-) or carboxymethylaminomethyl (cmnm-) groups at C5 of uracil base, are widely conserved at the 34th position of many prokaryotic tRNAs. In Gram-negative bacteria such as Escherichia coli, a bifunctional MnmC is involved in the last two reactions of the biosynthesis of mnm5(s2)U, in which the enzyme first converts cmnm5(s2)U to 5-aminomethyl-(2-thio)uridine (nm5(s2)U) and subsequently installs the methyl group to complete the formation of mnm5(s2)U. Although mnm5s2U has been identified in tRNAs of Gram-positive bacteria and plants as well, their genomes do not contain an mnmC ortholog and the gene(s) responsible for this modification is unknown. We discovered that MnmM, previously known as YtqB, is the methyltransferase that converts nm5s2U to mnm5s2U in Bacillus subtilis through comparative genomics, gene complementation experiments, and in vitro assays. Furthermore, we determined X-ray crystal structures of MnmM complexed with anticodon stem loop of tRNAGln. The structures provide the molecular basis underlying the importance of U33-nm5s2U34-U35 as the key determinant for the specificity of MnmM.

PubMed: 36762482
DOI: 10.1093/nar/gkad048

Experimental method

X-RAY DIFFRACTION (2.9 Å)