5EAQ

Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+

5EAQ の概要

• エントリーDOI: 10.2210/pdb5eaq/pdb
• 関連するPDBエントリー: 5EAO
• 分子名称: RNA (48-MER), RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'), MANGANESE (II) ION (3 entities in total)
• 機能のキーワード: ribozyme, hammerhead, rna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 22366.75

構造登録者

Mir, A.,Golden, B.L. (登録日: 2015-10-16, 公開日: 2016-02-24, 最終更新日: 2023-09-27)

主引用文献

Mir, A.,Golden, B.L.
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.
Biochemistry, 55:633-636, 2016

PubMed Abstract: The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

PubMed: 26551631
DOI: 10.1021/acs.biochem.5b01139

実験手法

X-RAY DIFFRACTION (3.201 Å)