2FIJ

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)

2FIJ の概要

• エントリーDOI: 10.2210/pdb2fij/pdb
• 関連するPDBエントリー: 2FIH 2FII 2FIL
• 分子名称: 5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3', CHLORIDE ION, COBALT HEXAMMINE(III), ... (4 entities in total)
• 機能のキーワード: arabinonucleic acid, sugar modifications, a-form dna, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6672.81

構造登録者

Egli, M.,Li, F. (登録日: 2005-12-29, 公開日: 2006-05-23, 最終更新日: 2023-08-30)

主引用文献

Li, F.,Sarkhel, S.,Wilds, C.J.,Wawrzak, Z.,Prakash, T.P.,Manoharan, M.,Egli, M.
2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
Biochemistry, 45:4141-4152, 2006

PubMed Abstract: 2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

PubMed: 16566588
DOI: 10.1021/bi052322r

実験手法

X-RAY DIFFRACTION (1.19 Å)