Molecular basis of the recognition of FMN by a HAD phosphatase TON_0338

The haloalkaloic acid dehalogenase (HAD) phosphatase from Thermococcus onnurineus NA1 (TON_0338), has phosphatase activity the flavin mono-nucleotide (FMN). The molecular origin and structural motifs for the activity deficiency of double-tryptophan mutant have not been rationalized at atomic resolution. Molecular dynamics (MD) simulations and the molecular mechanics/Generalized-Born surface area (MM/GBSA) free energy calculations were used to explore the effects of mutations on the changes in both structural flexibility and conformational dynamics. The non-polar solvation energy plays an indispensable role in the binding process of TON_0338 and FMN. The tryptophan sandwich structure provides a primary function to anchor FMN and keeps FMN well bound to TON_0338. The double-tryptophan mutation has influences on the secondary structures of TON_0338 and changes the conformation, which would lead to reduced activity of W58A/W61A-FMN binding. The present study provides important insights into the structure-function relationships of TON_0338 protein, which could contribute to further understanding about the HAD phosphatases.