Molecular dynamic simulation was done, in neutral and acidic conditions mimicking through protonation of the surface accessible residues, on Aspergillus niger esterase (EstA) to get an insight of the domain movement of the protein. The structure was taken from protein databank under pdb Id 1UKC. It has hydrolase superfold with catalytic triad as Ser210, Glu338 and His440. Simulation studies revealed larger fluctuations of EstA residues in acidic environment as compared to neutral environment, the conformation of protein changed from closed to open form at acidic conditions whereas at neutral conditions enzyme was in closed conformation. Movements in residues of regulatory domain were found responsible for the correct conformation and proper orientation of active site residues. Absence of lid domain was also seen during simulation. Simulation of Rhizomucor mehei lipase was also performed at an acidic pH for comparative analysis.