3RK4

Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31

3RK4 の概要

• エントリーDOI: 10.2210/pdb3rk4/pdb
• 関連するPDBエントリー: 1BN6 1CQW 3FBW 3FWH 3G9X 3RLT
• 分子名称: Haloalkane dehalogenase, CHLORIDE ION (3 entities in total)
• 機能のキーワード: catalytic pentad, alpha/beta-hydrolase fold, hydrolase, halide binding, hydrolytic dehalogenation
• 由来する生物種: Rhodococcus rhodochrous
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34272.41

構造登録者

Lahoda, M.,Stsiapanava, A.,Mesters, J.,Chaloupkova, R.,Damborsky, J.,Kuta Smatanova, I. (登録日: 2011-04-17, 公開日: 2012-04-18, 最終更新日: 2023-09-13)

主引用文献

Lahoda, M.,Mesters, J.R.,Stsiapanava, A.,Chaloupkova, R.,Kuty, M.,Damborsky, J.,Kuta Smatanova, I.
Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.
Acta Crystallogr.,Sect.D, 70:209-217, 2014

PubMed Abstract: Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in the aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here, the 1.31 Å resolution crystal structure of substrate-free DhaA31, the 1.26 Å resolution structure of DhaA31 in complex with TCP and the 1.95 Å resolution structure of wild-type DhaA are reported. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir after crystallization at pH 6.5 and room temperature. Comparison of the substrate-free structure with that of the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the active site of the enzyme indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the DhaA31 variant with wild-type DhaA revealed that the introduced substitutions reduce the volume and the solvent-accessibility of the active-site pocket.

PubMed: 24531456
DOI: 10.1107/S1399004713026254

実験手法

X-RAY DIFFRACTION (1.31 Å)