3TP4

Crystal Structure of engineered protein at the resolution 1.98A, Northeast Structural Genomics Consortium Target OR128

3TP4 の概要

• エントリーDOI: 10.2210/pdb3tp4/pdb
• 関連するPDBエントリー: 2BVY
• 分子名称: computational Design of Enzyme, ACETIC ACID, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: structural genomics, psi-biology, protein structure initiative, northeast structural genomics consortium, nesg, or128, osh97, unknown function
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 100611.08

構造登録者

Kuzin, A.,Su, M.,Seetharaman, J.,Rajagopalan, S.,Everett, J.K.,Nair, R.,Acton, T.B.,Rost, B.,Baker, D.,Montelione, G.T.,Hunt, J.F.,Tong, L.,Northeast Structural Genomics Consortium (NESG) (登録日: 2011-09-07, 公開日: 2011-10-05, 最終更新日: 2024-11-06)

主引用文献

Rajagopalan, S.,Wang, C.,Yu, K.,Kuzin, A.P.,Richter, F.,Lew, S.,Miklos, A.E.,Matthews, M.L.,Seetharaman, J.,Su, M.,Hunt, J.F.,Cravatt, B.F.,Baker, D.
Design of activated serine-containing catalytic triads with atomic-level accuracy.
Nat.Chem.Biol., 10:386-391, 2014

PubMed Abstract: A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.

PubMed: 24705591
DOI: 10.1038/nchembio.1498

実験手法

X-RAY DIFFRACTION (1.979 Å)