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Protein Science (2005), 14:395-400. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Crystal structure of the complex formed between a group I Phospholipase A2 and a naturally occurring fatty acid at 2.7 Å resolution

Garima Singh, Jayasankar Jasti, K. Saravanan, Sujata Sharma, Punit Kaur, A. Srinivasan and Tej P. Singh

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India

(RECEIVED September 11, 2004; FINAL REVISION October 1, 2004; ACCEPTED October 1, 2004)

This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A2 (PLA2) and also to a PLA2 with Asp 49. The fatty acid identified as n-tridecanoic acid is observed at the substrate recognition site of PLA2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA2 was determined using the cDNA method. Three-dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 Å. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n-tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium-binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n-tridecanoic acid was clearly fitted. The MALDI–TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA2 by 212 Da over the native PLA2. A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium-binding loop.

Keywords: n-tridecanoic acid; PLA2 complex; crystal structure; regulation

Abbreviations: PLA2, Phospholipase A2 • PDB, Protein Data Bank • rms, root-mean-square • SDS-PAGE, sodium dodecyl sulphate-polyacrylamide gel electrophoresis • CNS, Crystallography & NMR systems • MALDI–TOF, matrix-assisted laser desorption/ionization–time of flight

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041115505.

Reprint requests to: Tej P. Singh, Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India; e-mail: tps{at}aiims.aiims.ac.in; fax: 91-11-2658 8663.


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