8H0S

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

8H0S の概要

• エントリーDOI: 10.2210/pdb8h0s/pdb
• 分子名称: 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)
• 機能のキーワード: methyltransferase, trna post-transcriptional modification, mnmc mnm5(s2)u, transferase-rna complex, transferase/rna
• 由来する生物種: Bacillus subtilis subsp. subtilis str. 168; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 101367.21

構造登録者

Kim, J.,Lee, J.,Cho, G. (登録日: 2022-09-30, 公開日: 2023-01-25, 最終更新日: 2023-10-25)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.9 Å)