5D1O

Archaeal ATP-dependent RNA ligase - form 1

5D1O の概要

• エントリーDOI: 10.2210/pdb5d1o/pdb
• 関連するPDBエントリー: 5D1P
• 分子名称: ATP-dependent RNA ligase, ADENOSINE-5'-TRIPHOSPHATE, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: atp-dependent rna ligase, archaea, ligase
• 由来する生物種: Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 87061.18

構造登録者

Murakami, K.S. (登録日: 2015-08-04, 公開日: 2016-03-09, 最終更新日: 2025-04-02)

主引用文献

Gu, H.,Yoshinari, S.,Ghosh, R.,Ignatochkina, A.V.,Gollnick, P.D.,Murakami, K.S.,Ho, C.K.
Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.
Nucleic Acids Res., 44:2337-2347, 2016

PubMed Abstract: An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (MthRnl) catalyzes intramolecular ligation of single-stranded RNA to form a closed circular RNA via covalent ligase-AMP and RNA-adenylylate intermediate. Here, we report the X-ray crystal structures of an MthRnl•ATP complex as well as the covalent MthRnl-AMP intermediate. We also performed structure-guided mutational analysis to survey the functions of 36 residues in three component steps of the ligation pathway including ligase-adenylylation (step 1), RNA adenylylation (step 2) and phosphodiester bond synthesis (step 3). Kinetic analysis underscored the importance of motif 1a loop structure in promoting phosphodiester bond synthesis. Alanine substitutions of Thr117 or Arg118 favor the reverse step 2 reaction to deadenylate the 5'-AMP from the RNA-adenylate, thereby inhibiting step 3 reaction. Tyr159, Phe281 and Glu285, which are conserved among archaeal ATP-dependent RNA ligases and are situated on the surface of the enzyme, are required for RNA binding. We propose an RNA binding interface of the MthRnl based on the mutational studies and two sulfate ions that co-crystallized at the active site cleft in the MthRnl-AMP complex.

PubMed: 26896806
DOI: 10.1093/nar/gkw094

実験手法

X-RAY DIFFRACTION (2.648 Å)