Structure of an acidic phospholipase A(2) from the venom of Deinagkistrodon acutus in a new crystal form.
The three-dimensional structure of an acidic phospholipase A(2) 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 PLA(2)s 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.
Gu
L C
LC
National Laboratory of Biomacromolecules, Institute of Biophysics, the Chinese Academy of Sciences, Beijing 100101, China. lin@sun5.ibp.ac.cn
Zhang
H L
HL
Song
S Y
SY
Zhou
Y C
YC
Lin
Z J
ZJ
D017836:Agkistrodon; D000595:Amino Acid Sequence; D000818:Animals; D002118:Calcium / Q000737:chemistry; D003435:Crotalid Venoms / Q000737:chemistry / Q000201:enzymology*; D003460:Crystallization; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010741:Phospholipases A / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
D003435:Crotalid Venoms; D010741:Phospholipases A; D002118:Calcium