title: Structural and functional role of water molecules in bovine pancreatic phospholipase A(2): a data-mining approach.
abstract: The water molecules in 25 (21 high-resolution and four atomic resolution) crystal structures of bovine pancreatic phospholipase A(2) have been analyzed in order to identify the invariant water molecules and their possible roles. A total of 24 water molecules have been identified that are invariant in all 25 crystal structures examined. These include the catalytic water molecule, which is directly involved in the enzyme mechanism, and the conserved structural water molecule, which stabilizes the extended hydrogen-bonding network of the active site. Furthermore, many other water molecules stabilize the structure, whilst a few have been found to maintain the active-site geometry and provide coordination to the functionally important calcium ion. The invariant water molecules have been carefully examined and their possible roles in the structure and/or function are discussed. Molecular-dynamics studies of all 25 crystal structures have also been carried out and the results provide a good explanation of and support the findings obtained from the crystal structures.
authors.affiliation: Bioinformatics Centre (Centre of Excellence in Structural Biology and Biocomputing), Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Shankar Prasad
authors.initials: SP
authors.lastname: Kanaujia
authors.forename: Kanagaraj
authors.initials: K
authors.lastname: Sekar
mesh_terms: D000818:Animals; D020134:Catalytic Domain / Q000235:genetics; D002417:Cattle; D003460:Crystallization; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D010179:Pancreas / Q000201:enzymology*; D054467:Phospholipases A2 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040681:Structural Homology, Protein; D014867:Water / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011994:Recombinant Proteins; D014867:Water; D054467:Phospholipases A2