8B5O

Structure of haloalkane dehalogenase DmmarA from Mycobacterium marinum at pH 5.5

Summary for 8B5O

• Entry DOI: 10.2210/pdb8b5o/pdb
• Descriptor: Haloalkane dehalogenase DhaA, GLYCEROL, FORMIC ACID, ... (5 entities in total)
• Functional Keywords: haloalkane dehalogenase, enzyme, hydrolase
• Biological source: Mycobacterium marinum
• Total number of polymer chains: 4
• Total formula weight: 134207.78

Authors

Snajdarova, K.,Marek, M. (deposition date: 2022-09-23, release date: 2023-08-30, Last modification date: 2024-03-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.597 Å)