6TFF

Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide (NAD+)

6TFF の概要

• エントリーDOI: 10.2210/pdb6tff/pdb
• 分子名称: Chains: A, MAGNESIUM ION, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: rna structure; riboswitch; x-ray crystallography, non-coding rna, rna
• 由来する生物種: Candidatus Koribacter versatilis Ellin345
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 17752.81

構造登録者

Huang, L.,Lilley, D.M.J. (登録日: 2019-11-14, 公開日: 2020-09-23, 最終更新日: 2024-01-24)

主引用文献

Huang, L.,Wang, J.,Lilley, D.M.J.
Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch.
Rna, 26:878-887, 2020

PubMed Abstract: The A motif is the first known NAD-dependent riboswitch, comprising two similar tandem bulged stem-loop structures. We have determined the structure of the 5' domain 1 of the riboswitch. It has three coaxial helical segments, separated by an ACANCCCC bulge and by an internal loop, with a tertiary contact between them that includes two C:G base pairs. We have determined the structure with a number of ligands related to NADH, but in each case only the ADP moiety is observed. The adenosine adopts an conformation, forms multiple hydrogen bonds across the width of the sugar edge of the penultimate C:G base pair of the helix preceding the bulge, and the observed contacts have been confirmed by mutagenesis and calorimetry. Two divalent metal ions play a key structural role at the narrow neck of the bulge. One makes direct bonding contacts to the diphosphate moiety, locking it into position. Thus the nucleobase, ribose, and phosphate groups of the ADP moiety are all specifically recognized by the RNA. The NAD riboswitch is modular. Domain 1 is an ADP binding domain that may be ancient and could potentially be used in combination with other ligand binding motifs such as CoA.

PubMed: 32295864
DOI: 10.1261/rna.074898.120

実験手法

X-RAY DIFFRACTION (2.52 Å)