Conformational dynamics of active site loop in Escherichia coli phytase

• Published in: Biopolymers Vol. 93; no. 11; pp. 994 - 1002
• Main Authors: Shivange, Amol V., Schwaneberg, Ulrich, Roccatano, Danilo
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.11.2010
• Subjects: 6-Phytase - chemistry; active site loop; Catalytic Domain; cluster analysis; Crystallography, X-Ray; domainselect analysis; Escherichia coli - enzymology; Models, Molecular; Molecular Dynamics Simulation; molecular dynamics simulations; phytase; principal component analysis; Protein Conformation
• ISSN: 0006-3525; 1097-0282
• DOI: 10.1002/bip.21513

Phytases catalyze the release of phosphate by stepwise hydrolysis of phytate, a major source of phosphate in cereal grains, legumes, and oilseeds. Phytase improves, as a feed supplement, the nutritional quality of phytate rich diets and eventually reduce environmental pollution. Recently, phytases from enterobacteriaceae family have attracted industrial interest due to their high specific activity (2500–4000 U/mg). However, only limited information is available concerning structural dynamics of this class of enzymes. In this study, 50 nanosecond molecular dynamics simulation was performed on two Escherichia coli phytase structures (closed and open active site loop) to investigate conformational dynamics of the active site loop. Cluster analysis and principal component analysis (PCA) reveal significant difference in the conformational dynamics of active site compared to reported crystal structure. Molecular dynamic studies indicated that the movement in the active site of E. coli phytase is mainly confined by the active site loop resulted in wider opening of the loop in absence of phytate. The molecular dynamics studies highlight the possible role of loop residues as prerequisite for highly active phytases. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 994–1002, 2010.