5FQQ

Last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A

5FQQ の概要

• エントリーDOI: 10.2210/pdb5fqq/pdb
• 関連するPDBエントリー: 5FQI 5FQJ 5FQK
• 分子名称: GNCA4 LACTAMASE, 2-(2-METHOXYETHOXY)ETHANOL, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• 機能のキーワード: hydrolase, precambrian, resurrected beta-lactamase, gnca4
• 由来する生物種: SYNTHETIC CONSTRUCT
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 29228.99

構造登録者

Gavira, J.A.,Martinez-Rodriguez, S.,Risso, V.A.,Sanchez-Ruiz, J.M. (登録日: 2015-12-14, 公開日: 2016-12-28, 最終更新日: 2024-01-10)

主引用文献

Risso, V.A.,Martinez-Rodriguez, S.,Candel, A.M.,Kruger, D.M.,Pantoja-Uceda, D.,Ortega-Munoz, M.,Santoyo-Gonzalez, F.,Gaucher, E.A.,Kamerlin, S.C.L.,Bruix, M.,Gavira, J.A.,Sanchez-Ruiz, J.M.
De novo active sites for resurrected Precambrian enzymes.
Nat Commun, 8:16113-16113, 2017

PubMed Abstract: Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

PubMed: 28719578
DOI: 10.1038/ncomms16113

実験手法

X-RAY DIFFRACTION (2.12 Å)