Journal:Acta Cryst D:S2059798323006642

Atypical Homodimerisation Revealed by the Structure of (S)-Enantioselective Haloalkane Dehalogenase DmmarA from Mycobacterium marinum

Karolina Snajdarova, Sérgio M. Marques, Jiri Damborsky, David Bednar, Martin Marek ^[1]

Molecular Tour
Haloalkane dehalogenases are a family of alpha/beta-hydrolase fold enzymes employing SN2 nucleophilic substitution to cleave the carbon-halogen bond in diverse chemical structures, whose biological role is still poorly understood. Atomic-level knowledge of both the inner organization and supramolecular complexation of HLDs is thus crucial for our understanding of their catalytic and non-catalytic functions. Here, we determined crystallographic structures of an (S)-enantioselective haloalkane dehalogenase DmmarA from the waterborne pathogenic microbe Mycobacterium marinum at 1.6 Å and 1.85 Å resolutions. The structures show a canonical αβα-sandwich HLD fold with several unusual structural features. Mechanistically, the atypical composition of a proton-relay catalytic triad (aspartate-histidine-aspartate) and uncommon active site pocket expose molecular specificities of catalytic apparatus that exhibits rare (S)-enantiopreference. Additionally, the structures reveal an as-yet-unseen mode of symmetric homodimerization, which is predominantly mediated through unusual L5-to-L5 loops interactions. This homodimeric association in a 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 variances in the activation barrier of nucleophilic substitution.

References

1. ↑ doi: https://dx.doi.org/10.1107/S2059798323006642