1TC8

Crystal structure of Krait-venom phospholipase A2 in a complex with a natural fatty acid tridecanoic acid

Summary for 1TC8

• Entry DOI: 10.2210/pdb1tc8/pdb
• Related: 1FE5
• Descriptor: phospholipase A2 isoform 1, SODIUM ION, N-TRIDECANOIC ACID, ... (4 entities in total)
• Functional Keywords: phospholipasea2, complex, crystal, fatty acid, toxin
• Biological source: Bungarus caeruleus
• Total number of polymer chains: 1
• Total formula weight: 13451.12

Authors

Singh, G.,Jasti, J.,Saravanan, K.,Sharma, S.,Kaur, P.,Srinivasan, A.,Singh, T.P. (deposition date: 2004-05-21, release date: 2004-06-08, Last modification date: 2024-10-30)

Primary citation

Singh, G.,Jasti, J.,Saravanan, K.,Sharma, S.,Kaur, P.,Srinivasan, A.,Singh, T.P.
Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution
PROTEIN SCI., 14:395-400, 2005

PubMed Abstract: 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 A. 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.

PubMed: 15659372
DOI: 10.1110/ps.041115505

Experimental method

X-RAY DIFFRACTION (2.7 Å)