Regulation of catalytic function by molecular association: structure of phospholipase A₂fromDaboia russelli pulchella(DPLA₂) at 1.9 Å resolution

Abstract

The crystal structure of phospholipase A 2 from the venom of Daboia russelli pulchella has been re®ned to an R factor of 0.216 using 17 922 re¯ections to 1.9 A Ê resolution. The structure contains two crystallographically independent molecules in the asymmetric unit. The overall conformations of the two molecules are essentially the same except for three regions, namely the calcium-binding loop including Trp31, the -wing and the C-terminal residues 119±131. Although these differences have apparently been caused by molecular packing, they seem to have functional relevance. Particularly noteworthy is the conformation of Trp31, which is favourable for substrate binding in one molecule as it is aligned with one of the side walls of the hydrophobic channel, whereas in the other molecule it is located at the mouth of the channel, thereby blocking the entry of substrates leading to loss of activity. This feature is unique to the present structure and does not occur in the dimers and trimers of other PLA 2 s.

Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS)

“…As reported previously (Chandra et al, 2001), two molecules of DPLA 2 were found to be strongly associated in both crystalline and solution states even at very low concentrations. However, every new preparation of DPLA 2 was examined for molecular association using the DLS system (Dlerks & Partner, Hamburg, Germany) and analyzed using the software described by Schulze (1996).…”

“…Both of these effects in DPLA 2 can be caused by the association of two molecules. Indeed, it has been shown by earlier studies (Chandra et al, 2000(Chandra et al, , 2001) that the association of two molecules converts the binding site of molecule A, which is located at the interface, into a suitable form of conformation for the binding of ligands, but not the binding site of molecule B. These studies have also shown that the surface-exposed hydrophobic channel in molecule B seems to be completely unin¯uenced by the association and hence the observed unsuitable conformation of the hydrophobic channel may be an inherent property of DPLA 2 .…”

“…The structure was obtained by the molecular-replacement method using the structure of DPLA 2 determined previously at 1.9 A Ê resolution (Chandra et al, 2001). The structure contains two molecules of DPLA 2 in the asymmetric unit, designated molecules A and B.…”

Crystal Structure of a Complex Formed between a Snake Venom Phospholipase A2 and a Potent Peptide Inhibitor Phe-Leu-Ser-Tyr-Lys at 1.8 Å Resolution

“…It may be emphasized that the peptide FLSYK forms a larger number of interactions with PLA 2 as compared with those observed in other complexes formed between PLA 2 and synthetic/natural inhibitors reported earlier (10,11,(13)(14)(15)(16)(37)(38)(39)(40)(41) making it to be the strongest inhibitor known so far against PLA 2 . Its dissociation constant, K d was found to be 3.57 Ϯ 0.05 ϫ 10 Ϫ9 M. Recently, molecular modeling studies showing the binding of FLSYK to human sPLA 2 -IIA were also reported (19).…”

“…The structure of PLA 2 from Daboia russelli pulchella has been studied in its native form (24) and in the complexed forms with natural substances such as ␣-tocopherol (39) and aristolochic acid (40), and with a designed peptide inhibitor Leu-Ala-IleTyr-Ser (LAIYS) (41). In all these structures, PLA 2 exists in the form of an asymmetric dimer.…”