6QKU

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Tyr219Phe - Chloroacetate soaked 2hr

6QKU の概要

• エントリーDOI: 10.2210/pdb6qku/pdb
• 分子名称: Fluoroacetate dehalogenase, chloroacetic acid, GLYCOLIC ACID, ... (5 entities in total)
• 機能のキーワード: hydrolaser, substrate inhibition, allostery, dynamics, hydrolase
• 由来する生物種: Rhodopseudomonas palustris
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 68451.27

構造登録者

Mehrabi, P.,Kim, T.H.,Prosser, R.S.,Pai, E.F. (登録日: 2019-01-30, 公開日: 2019-06-26, 最終更新日: 2023-11-15)

主引用文献

Mehrabi, P.,Di Pietrantonio, C.,Kim, T.H.,Sljoka, A.,Taverner, K.,Ing, C.,Kruglyak, N.,Pomes, R.,Pai, E.F.,Prosser, R.S.
Substrate-Based Allosteric Regulation of a Homodimeric Enzyme.
J.Am.Chem.Soc., 141:11540-11556, 2019

PubMed Abstract: Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.

PubMed: 31188575
DOI: 10.1021/jacs.9b03703

実験手法

X-RAY DIFFRACTION (1.511 Å)