3WVK

Time-Resolved Crystal Structure of HindIII with 230sec soaking

3WVK の概要

• エントリーDOI: 10.2210/pdb3wvk/pdb
• 関連するPDBエントリー: 3WVG 3WVH 3WVI 3WVP
• 分子名称: Type-2 restriction enzyme HindIII, DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3'), DNA (5'-D(*GP*CP*CP*A)-3'), ... (7 entities in total)
• 機能のキーワード: freeze-trap, time-resolved, type iip restriction endonuclease, restriction endonuclease, hydrolase, nuclease, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Haemophilus influenzae; 詳細
• タンパク質・核酸の鎖数: 16
• 化学式量合計: 169927.88

構造登録者

Kawamura, T.,Kobayashi, T.,Watanabe, N. (登録日: 2014-05-22, 公開日: 2015-04-08, 最終更新日: 2023-11-08)

主引用文献

Kawamura, T.,Kobayashi, T.,Watanabe, N.
Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
Acta Crystallogr.,Sect.D, 71:256-265, 2015

PubMed Abstract: In order to investigate the mechanism of the reaction catalyzed by HindIII, structures of HindIII-DNA complexes with varying durations of soaking time in cryoprotectant buffer containing manganese ions were determined by the freeze-trap method. In the crystal structures of the complexes obtained after soaking for a longer duration, two manganese ions, indicated by relatively higher electron density, are clearly observed at the two metal ion-binding sites in the active site of HindIII. The increase in the electron density of the two metal-ion peaks followed distinct pathways with increasing soaking times, suggesting variation in the binding rate constant for the two metal sites. DNA cleavage is observed when the second manganese ion appears, suggesting that HindIII uses the two-metal-ion mechanism, or alternatively that its reactivity is enhanced by the binding of the second metal ion. In addition, conformational change in a loop near the active site accompanies the catalytic reaction.

PubMed: 25664735
DOI: 10.1107/S1399004714025188

実験手法

X-RAY DIFFRACTION (2 Å)