5DHC

Cooperativity and Downstream Binding in RNA Replication

5DHC の概要

• エントリーDOI: 10.2210/pdb5dhc/pdb
• 関連するPDBエントリー: 5DHB 5HBW 5HBX 5HBY 5KRG 5L00
• 分子名称: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3'), MAGNESIUM ION, GUANOSINE-5'-MONOPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: rna, monomer, cooperativity
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 21205.39

構造登録者

Zhang, W.,Fahrenbach, A.C.,Tam, C.P.,Szostak, J.W. (登録日: 2015-08-30, 公開日: 2016-12-07, 最終更新日: 2023-09-27)

主引用文献

Zhang, W.,Tam, C.P.,Wang, J.,Szostak, J.W.
Unusual Base-Pairing Interactions in Monomer-Template Complexes.
ACS Cent Sci, 2:916-926, 2016

PubMed Abstract: Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer-template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5'-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer-template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson-Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3' of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson-Crick base pairing between monomers and primer-template complexes, and by bringing the reactive functional groups into closer proximity.

PubMed: 28058281
DOI: 10.1021/acscentsci.6b00278

実験手法

X-RAY DIFFRACTION (1.55 Å)