Structure of an Acidic Phospholipase A₂ from the Venom of Deinagkistrodon acutus in a New Crystal Form

GU Li-Chuan, ZHANG Hai-Long, SONG Shi-Ying, ZHOU Yuan-Cong¹, LIN Zheng-Jiong^*
( National Laboratory of Biomacromolecules, Institute of Biophysics, the Chinese Academy of Sciences, Beijing 100101, China; ¹Institute of Biochemistry and Cell Biology, the Chinese Academy of Sciences, Shanghai 200031, China )

Abstract    The three-dimensional structure of an acidic phospholipase A₂ purified from the venom of Deinagkistrodon acutus (Agkistrodon acutus) was determined in a new crystal form by molecular replacement at 0.28 nm resolution with a crystallographic R factor of 21.9% (R-free=25.7%) and reasonable stereochemistry. Being similar to the previous reported crystal form, a significant conformational adaptation of segment 14—23 at the dimer interface was observed. This segment was related to the “interface recognition site” (IRS). It was found that a positively charged residue at position 34 seems to be a common feature for most of hemolytic PLA₂s belonging to group II. Structural comparison between the two crystal forms showed that NaCl had significant effects on the crystal packing, thus leading to dramatic changes of the unit cell parameters. In the new crystal form, MPD (2-methyl-2, 4-pentanediol) molecules exist in the hydrophobic channel of the enzyme.
Key words    phospholipase A₂; X-ray crystallography; three-dimensional structure; hemolysis; interfacial catalysis

^*Corresponding author: Tel, 86-10-64888513; Fax, 86-10-64877837; e-mail, [email protected]