7KUN

2'-F modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G

7KUN の概要

• エントリーDOI: 10.2210/pdb7kun/pdb
• 分子名称: RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*(GF2))-3'), DIGUANOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: rna, nonenzymatic rna extension
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 10640.88

構造登録者

Fang, Z.,Giurgiu, C.,Szostak, J.W. (登録日: 2020-11-25, 公開日: 2021-09-08, 最終更新日: 2023-10-18)

主引用文献

Giurgiu, C.,Fang, Z.,Aitken, H.R.M.,Kim, S.C.,Pazienza, L.,Mittal, S.,Szostak, J.W.
Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.
Angew.Chem.Int.Ed.Engl., 60:22925-22932, 2021

PubMed Abstract: The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.

PubMed: 34428345
DOI: 10.1002/anie.202109714

実験手法

X-RAY DIFFRACTION (1.58 Å)