Lipases from Bacillus thermocatenulatus are a member of superfamily of α/β hydrolase, but there are structural differences between them. In this work, we focused on the α5 helix of B. thermocatenulatus lipase (BTL2) which is absent in canonical α/β hydrolase fold. In silico study showed that the α5 helix is a region that causes disorder in BTL2 protein. So, the α5 helix (residues 131 to 150) has been deleted from the B. thermocatenulatus lipase gene (BTL2) and the remain (Δα5-BTL2) has been expressed in Pichia pastoris yeast. The α5 deletion results in increase of enzyme-specific activity in the presence of tributyrin, tricaproin, tricaprylin, tricaprin, trilaurin, and olive oil (C18) substrates by 1.4-, 1.7-, 2.0-, 1.2-, 1.75-, and 1.95-fold, respectively. Also, deletion leads to increase in enzyme activity in different temperatures and pHs, whereas it did not significantly affect on enzyme activity in the presence of organic solvents, metal ions, and detergents.