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Crystal structure of the complex formed between a group I Phospholipase A 2 and a naturally occurring fatty acid at 2.7 Å resolution
Author(s) -
Singh Garima,
Jasti Jayasankar,
Saravanan K.,
Sharma Sujata,
Kaur Punit,
Srinivasan A.,
Singh Tej P.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041115505
Subject(s) - chemistry , crystal structure , group (periodic table) , fatty acid , resolution (logic) , crystallography , crystal (programming language) , stereochemistry , biochemistry , organic chemistry , computer science , artificial intelligence , programming language
This is the first evidence of a naturally bound fatty acid to a group I Phospholipase A 2 (PLA 2 ) and also to a PLA 2 with Asp 49. The fatty acid identified as n ‐tridecanoic acid is observed at the substrate recognition site of PLA 2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA 2 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 PLA 2 by 212 Da over the native PLA 2 . 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 PLA 2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium‐binding loop.