Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum
| Authors | |
|---|---|
| Year of publication | 2023 |
| Type | Article in Periodical |
| Magazine / Source | Acta Crystallographica Section D: Structural Biology |
| MU Faculty or unit | |
| Citation | |
| Web | https://journals.iucr.org/d/issues/2023/11/00/jc5060/index.html |
| Doi | http://dx.doi.org/10.1107/S2059798323006642 |
| Keywords | haloalkane dehalogenases; Mycobacterium marinum; DmmarA; homodimerization; surface loops; enantioselectivity; X-ray crystallography; SAXS |
| Attached files | |
| Description | Haloalkane dehalogenases (HLDs) are a family of alpha/beta-hydrolase fold enzymes that employ S(N)2 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 angstrom resolution. The structures show a canonical alpha beta alpha-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. |
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