In Silico Analysis of Primary Sequence and Tertiary Structure of Lepidium Draba Peroxidase

Peroxidase enzymes are vastly applicable in industry and diagnosiss. Recently, we introduced a new kind of peroxidase gene from Lepidium draba (LDP). According to protein multiple sequence alignment results, LDP had 93% similarity and 88.96% identity with horseradish peroxidase C1A (HRP C1A). In the current study we employed in silico tools to determine, to which group of peroxidase enzymes LDP belongs. The tertiary structure of protein was built using homology modeling method and the overall quality of predicted model was evaluated. The physicochemical and spatial properties of protein were measured. The binding site of protein which made a motif, was determined. The predicted tertiary structure possesses acceptable quality, based on several criteria. The predicted motif was also in agreement with previous studies. The isoelectric point (pI) of LDP was calculated as 8.25. Due to neutral pI of LDP and high similarity between structure of LDP and HRP C1A, it is assumed that LDP belongs to the neutral or neutral-basic isoenzymes.