3BO4

A relaxed active site following exon ligation by a group I intron

3BO4 の概要

• エントリーDOI: 10.2210/pdb3bo4/pdb
• 関連するPDBエントリー: 3BO2 3BO3
• 分子名称: Group I intron P9, DNA/RNA (5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*A)-D(P*DG)-3'), DNA/RNA (5'-R(*CP*A)-D(P*DU)-R(P*AP*CP*GP*GP*CP*C)-3'), ... (7 entities in total)
• 機能のキーワード: group i intron, azoarcus, ribozyme, ligation, acetylation, mrna processing, mrna splicing, nucleus, ribonucleoprotein, rna-binding, spliceosome, nuclear protein-rna complex, nuclear protein/rna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P09012
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 83545.16

構造登録者

Lipchock, S.V.,Strobel, S.A. (登録日: 2007-12-17, 公開日: 2008-04-01, 最終更新日: 2024-02-21)

主引用文献

Lipchock, S.V.,Strobel, S.A.
A relaxed active site after exon ligation by the group I intron
Proc.Natl.Acad.Sci.Usa, 105:5699-5704, 2008

PubMed Abstract: During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

PubMed: 18408159
DOI: 10.1073/pnas.0712016105

実験手法

X-RAY DIFFRACTION (3.33 Å)