Structural and functional role of water molecules in bovine pancreatic phospholipase A(2): a data-mining approach

Kanaujia, Shankar Prasad and Sekar, Kanagaraj (2009) Structural and functional role of water molecules in bovine pancreatic phospholipase A(2): a data-mining approach. In: Acta Crystallographica Section D-Biological Crystallography, 65 (Part 1). pp. 74-84.

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Abstract

The water molecules in 25 (21 high-resolution and four atomic resolution) crystal structures of bovine pancreatic phospholipase A2 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.

Item Type:	Journal Article
Publication:	Acta Crystallographica Section D-Biological Crystallography
Publisher:	Blackwell Publishing
Additional Information:	Copyright of this article belongs to International Union of Crystallography.
Keywords:	bovine pancreatic phospholipase A2; water molecules; data mining
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	03 Nov 2009 09:11
Last Modified:	19 Sep 2010 05:00
URI:	http://eprints.iisc.ac.in/id/eprint/18145

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