Molecular Dynamics Simulations for the Michaelis Complex of Ectoine Synthase (EctC)

Ectoine is a chemical chaperone synthesised and used by bacteria to defend against osmotic stress. Although it has already gained attention from the pharmaceutical cosmetic industries, thanks its hydrating cell-protecting properties, reaction mechanism of final synthesis step still not fully understood. The ultimate ectoine biosynthesis catalysed synthase enzyme (EctC), which requires an iron ion for substrate binding overall enzymatic activity. Even though crystal structure Paenibacillus lautus EctC—substrate complex available (PDB: 5ONN), very informative with respect geometry active site because: (1) was obtained at pH value far enzyme’s optimum, (2) electron density Fe position weak, (3) Fe-ligand distances are too long. To fill this gap, in work we have classical molecular dynamics simulations model enzyme-substrate (N-gamma-acetyl-L-2,4-diaminobutyric acid) EctC (PlEctC). Since PlEctC homodimeric protein, MD were carried out dimer various plausible occupancies two coordination geometries around catalytic ion: tetrahedral octahedral. results revealed that presence ligand stabilising effect on protein structure, most notably short helix 112–118, flanks entrance site. important amino acids Trp21, Arg25, Asn38, Thr40, Tyr52, also identified structure. Importantly, can easily adopt conformation suitable progress reaction, does so spontaneously octahedral 6-coordinate cofactor or low energy penalty (ca. 3 kcal/mol) case 4-coordinate geometry. Simulations different occupancy states did reveal any signs cooperativity between monomers.