The Rieske dioxygenase system in Achromobacter: in silico studies of the protein structure and substrate interactions

Using a set of protein sequences of the class IIB Rieske dioxygenase system of the Achromobacter insolitus LCu2 strain, known for its ability to degrade pollutants, large-scale bioinformatic assessments of the potential of Achromobacter as an effective tool for bioremediation were performed. More than 100 homologues and isoforms of proteins in this system have been identified in various species of the genus Achromobacter. The reproducibility and stability of their 3D structures with ions and coenzymes, predicted using the AlphaFold 3 program, were established despite significant changes in protein sequences with a percentage identity of ≈ 20-99% within the genus. Using AlphaFold 3 and DeepPeptide programs and considering the experimental 3D structures of Rieske dioxygenase proteins of various bacterial classes from the PDB database, presumable propeptides were identified for the first time in achromobacteria at the N- and C-termini of the protein precursors. Their possible functions include participation in the folding, maturation, stabilization of proteins, and regulation of their activity. The genomic context of the proteins in the type strains of Achromobacter species revealed a conservative clustering pattern. Along with the stability of the protein 3D structures, this may contribute to the conservation of the functional activity of the enzymes as the strains adapt to their respective ecological niches. The interactions of the substrates with the enzyme and isoenzyme in the catalytic domain of the dioxygenase were characterized Using AutoDock Vina, which showed that their substrate specificity remained virtually unchanged. Overall, a wide range of Achromobacter strains suitable for biodegradation (bioremediation) was identified.