Study of structural variation at catalytic site of adenylate domain of iturin synthetase enzyme with respect to amino acid change

The geometrical and energetic variation at catalytic site of enzyme with respect to amino acid change is helpful to optimize the rate of catalysis of enzyme. In the present study, 22 iturin synthetase enzyme sequences comprised of 5 copies of iturin A, 8 copies of iturin B, 8 copies of iturin C and a single copy of iturin D of different strains of Bacillus amyloliquefaciens were retrieved and considered for structural variation study at catalytic site of AMP binding domain. A pattern derived from the Multiple sequence alignment was, [GAPH]-[LIPV]-X-[LIPV]-X-[IL]-[FTNR]-N-[EVH]-Y-G-P-T-E-[TN]-X-V-X[2,3]-[IVL] with a catalytic site pattern as, [N-E-Y-G-P-T-E]. A part of adenylate domain was separated from long iturin synthetase enzyme sequence and processed for 3D structure prediction by Homology modeling method on Phyre2 server. The obtained 3D protein structure were structurally aligned by MATRAS software. Structures were observed at catalytic site for structural variation with respect to amino acid change. Amino acid change at position 2 of pattern [N-E-Y-G-P-T-E], where Glu (E) is changed to either Val (V) or His (H) amino acid has increased the energy of adenylate domain of catalytic site of iturin synthetase turning it bit less stable, which was observed from the increase in energy of that amino acid and hence the total potential energy of enzyme. The variation in adjacent regions of conserved pattern was observed among the iturin synthetase adenylation domain of type A, B, C and D, indicating the variation of amino acids sequence in cyclic peptide, iturin molecule.