In silico structural analysis of a putative serine collagenase from Pseudolycoriella hygida (Diptera: Sciaridae)

Our laboratory uses as a model organism the insect Pseudolycoriella hygida, a Diptera of the Sciaridae family. In nature, sciarids live in the soil where they act as biomass decomposers. The Psl. hygida genome includes 242 genes encoding putative secreted peptidases, of which 152 belong to the serine peptidase family. These enzymes comprise a diverse family characterized by a catalytic serine located in a catalytic triad together with histidine, and aspartate residues. The S1A family includes trypsins, chymotrypsins, elastases, and serine collagenases, the latter being originally characterized by their ability to degrade collagen. This work aimed to apply 3D-structural prediction using AlphaFold to model a putative serine collagenase of Psl. hygida. Initially, pairwise sequence alignments were performed between the eight putative serine collagenases of Psl. hygida and previously characterized serine collagenases from Leptuca pugilator (AAC47030.1), Hypoderma lineatum (P08897.3), and Aedes aegypti (AAA29356.1). The Psl. hygida collagenase KAJ6642449.1 showed the highest sequence similarity and was selected for structural modeling with AlphaFold. The quality of predicted structure was analyzed using the SAVES v6.1 server (UCLA). The Ramachandran plot showed 90.5% of the residues were located in the most favored regions. PROCHECK analysis showed a G-factor of −0.1, the ERRAT score was 90.35, and Verify3D indicated that 70.59% of the residues had an acceptable 3D–1D profile. Together, these results indicate good overall quality of the AlphaFold model. The predicted structure was compared with the available structure of H. lineatum collagenase (P08897.3) by structural superposition using the MatchMaker tool in ChimeraX. The sequence alignment score between the Psl. hygida and H. lineatum collagenases was 566.2 and the RMSD calculated from 197 pruned atom pairs was 0.722 Å. In addition, the catalytic triad of the Psl. hygida collagenase is identical to that of H. lineatum and occupies a structurally conserved position within the protein. These results provide evidence for structural homology between the investigated serine collagenase of H. lineatum and Psl. hygida. This putative Psl. hygida serine collagenase was selected for heterologous expression in Komagataella phaffii.