6Y9E

Crystal structure of putative ancestral haloalkane dehalogenase AncHLD2 (node 2)

6Y9E の概要

• エントリーDOI: 10.2210/pdb6y9e/pdb
• 分子名称: Ancestral haloalkane dehalogenase AncHLD2, CHLORIDE ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (6 entities in total)
• 機能のキーワード: haloalkane dehalogenase, hydrolase
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 209445.60

構造登録者

Chaloupkova, R.,Damborsky, J.,Marek, M. (登録日: 2020-03-09, 公開日: 2020-11-18, 最終更新日: 2024-01-24)

主引用文献

Babkova, P.,Dunajova, Z.,Chaloupkova, R.,Damborsky, J.,Bednar, D.,Marek, M.
Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics.
Comput Struct Biotechnol J, 18:1497-1508, 2020

PubMed Abstract: Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (Δ up to 24 °C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts.

PubMed: 32637047
DOI: 10.1016/j.csbj.2020.06.021

実験手法

X-RAY DIFFRACTION (1.7 Å)