1QQ6

STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS WITH CHLOROACETIC ACID COVALENTLY BOUND

1QQ6 の概要

• エントリーDOI: 10.2210/pdb1qq6/pdb
• 関連するPDBエントリー: 1AQ6 1QQ5 1QQ7
• 分子名称: PROTEIN (L-2-HALOACID DEHALOGENASE), CHLORIDE ION (3 entities in total)
• 機能のキーワード: l-2 haloacid dehalogenase, hydrolase
• 由来する生物種: Xanthobacter autotrophicus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 55235.78

構造登録者

Ridder, I.S.,Rozeboom, H.J.,Kalk, K.H.,Dijkstra, B.W. (登録日: 1999-06-11, 公開日: 1999-10-25, 最終更新日: 2023-11-15)

主引用文献

Ridder, I.S.,Rozeboom, H.J.,Kalk, K.H.,Dijkstra, B.W.
Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.
J.Biol.Chem., 274:30672-30678, 1999

PubMed Abstract: The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoates to their corresponding D-2-hydroxyalkanoates, with inversion of the configuration at the C(2) atom. The structure of the apoenzyme at pH 8 was refined at 1.5-A resolution. By lowering the pH, the catalytic activity of the enzyme was considerably reduced, allowing the crystal structure determination of the complexes with L-2-monochloropropionate and monochloroacetate at 1.7 and 2.1 A resolution, respectively. Both complexes showed unambiguous electron density extending from the nucleophile Asp(8) to the C(2) atom of the dechlorinated substrates corresponding to a covalent enzyme-ester reaction intermediate. The halide ion that is cleaved off is found in line with the Asp(8) Odelta1-C(2) bond in a halide-stabilizing cradle made up of Arg(39), Asn(115), and Phe(175). In both complexes, the Asp(8) Odelta2 carbonyl oxygen atom interacts with Thr(12), Ser(171), and Asn(173), which possibly constitute the oxyanion hole in the hydrolysis of the ester bond. The carboxyl moiety of the substrate is held in position by interactions with Ser(114), Lys(147), and main chain NH groups. The L-2-monochloropropionate CH(3) group is located in a small pocket formed by side chain atoms of Lys(147), Asn(173), Phe(175), and Asp(176). The size and position of the pocket explain the stereospecificity and the limited substrate specificity of the enzyme. These crystallographic results demonstrate that the reaction of the enzyme proceeds via the formation of a covalent enzyme-ester intermediate at the nucleophile Asp(8).

PubMed: 10521454
DOI: 10.1074/jbc.274.43.30672

実験手法

X-RAY DIFFRACTION (2.1 Å)