8B5K

Structure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 6.5

8B5K の概要

• エントリーDOI: 10.2210/pdb8b5k/pdb
• 分子名称: Haloalkane dehalogenase DhaA, GLYCEROL, FORMIC ACID, ... (6 entities in total)
• 機能のキーワード: haloalkane dehalogenase, enzyme, hydrolase
• 由来する生物種: Mycobacterium marinum
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 134461.25

構造登録者

Snajdarova, K.,Marek, M. (登録日: 2022-09-23, 公開日: 2023-08-30, 最終更新日: 2024-03-13)

主引用文献

Snajdarova, K.,Marques, S.M.,Damborsky, J.,Bednar, D.,Marek, M.
Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum.
Acta Crystallogr D Struct Biol, 79:956-970, 2023

PubMed Abstract: Haloalkane dehalogenases (HLDs) are a family of α/β-hydrolase fold enzymes that employ S2 nucleophilic substitution to cleave the carbon-halogen bond in diverse chemical structures, the biological role of which is still poorly understood. Atomic-level knowledge of both the inner organization and supramolecular complexation of HLDs is thus crucial to understand their catalytic and noncatalytic functions. Here, crystallographic structures of the (S)-enantioselective haloalkane dehalogenase DmmarA from the waterborne pathogenic microbe Mycobacterium marinum were determined at 1.6 and 1.85 Å resolution. The structures show a canonical αβα-sandwich HLD fold with several unusual structural features. Mechanistically, the atypical composition of the proton-relay catalytic triad (aspartate-histidine-aspartate) and uncommon active-site pocket reveal the molecular specificities of a catalytic apparatus that exhibits a rare (S)-enantiopreference. Additionally, the structures reveal a previously unobserved mode of symmetric homodimerization, which is predominantly mediated through unusual L5-to-L5 loop interactions. This homodimeric association in solution is confirmed experimentally by data obtained from small-angle X-ray scattering. Utilizing the newly determined structures of DmmarA, molecular modelling techniques were employed to elucidate the underlying mechanism behind its uncommon enantioselectivity. The (S)-preference can be attributed to the presence of a distinct binding pocket and variance in the activation barrier for nucleophilic substitution.

PubMed: 37860958
DOI: 10.1107/S2059798323006642

実験手法

X-RAY DIFFRACTION (1.849 Å)