5D0A

Crystal structure of epoxyqueuosine reductase with cleaved RNA stem loop

5D0A の概要

• エントリーDOI: 10.2210/pdb5d0a/pdb
• 関連するPDBエントリー: 5D08 5D0B
• 分子名称: Epoxyqueuosine reductase, RNA (5'-R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'), IRON/SULFUR CLUSTER, ... (7 entities in total)
• 機能のキーワード: b12, trna modification, heat-domain, queuosine, oxidoreductase-rna complex, oxidoreductase/rna
• 由来する生物種: Bacillus subtilis (strain 168); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 214683.94

構造登録者

Dowling, D.P.,Miles, Z.D.,Kohrer, C.,Bandarian, V.,Drennan, C.L. (登録日: 2015-08-03, 公開日: 2016-09-28, 最終更新日: 2023-09-27)

主引用文献

Dowling, D.P.,Miles, Z.D.,Kohrer, C.,Maiocco, S.J.,Elliott, S.J.,Bandarian, V.,Drennan, C.L.
Molecular basis of cobalamin-dependent RNA modification.
Nucleic Acids Res., 44:9965-9976, 2016

PubMed Abstract: Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis Our structure of QueG bound to a tRNA anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.

PubMed: 27638883
DOI: 10.1093/nar/gkw806

実験手法

X-RAY DIFFRACTION (2.1 Å)