Bacterial luciferase is a flavin-dependent monooxygenase, which catalyzes the reaction with formation of electronically excited intermediate. The reaction requires а reduced flavin mononucleotide provided by the oxidoreductase and a long-chain aldehyde produced by the fatty acid reductase multienzyme complex. Bacterial luciferases from various luminous species have distinct structural properties and nonstationary reaction kinetics: the enzymes from Photobacterium and Aliivibrio speciesare conventionally called “fast” luciferases, while those from Vibrio and Photorhabdus species – “slow” ones. It is known that fatty acid reductase multienzyme complexes from bacteria with “fast” luciferases are specific to tetradecanal, while from the other luminous species – to decanal. The structural aspect of interaction between bacterial luciferases and aldehydes with various chains still remains unclear.

In current work the molecular docking simulation was performed to elucidate the binding mode of decanal, dodecanal and tetradecanal in the active site of bacterial luciferases using Autodock Vina. Two enzymes were studied: V. harveyi (PDB ID: 3FGC) and P. leiognathi. The tertiary structure of P. leiognathi luciferase was obtained by Swiss-MODEL server using homology modeling approach with the structure of V. harveyi luciferase as a template. 20 ns molecular dynamics simulation was performed for both structures at 298 K and a constant pressure of 1 atm in GROMACS (CHARMM36 force field). Then the β-subunit of the luciferase was removed and complex of a-subunit with flavin-4a-hydroperoxide was obtained using rigid molecular docking. The resulting structure was utilized for aldehyde docking.

From the docking results the aldehyde binding sites for two types of luciferases were unequivocally established. It was obtained that P. leiognathi luciferase binds tetradecanal with higher affinity than decanal, while V. harveyi luciferase exhibits a reversed pattern. Additionally both luciferases were found to fix the flavin-4a-hydroperoxide in a similar way in their active sites.

The study was supported by the project No16-14-10115.