The Crystal Structure of Prokaryotic Phospholipase A2

In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A2 (PLA2), produced extracellularly by Streptomyces violaceoruber, were determined by using the multiple isomorphous replacement and molecular replacement methods, respectively. The former and latter structures were refined to an R-factor of 18.8% at a 1.4-Å resolution and an R-factor of 15.0% at a 1.6-Å resolution, respectively. The overall structure of the prokaryotic PLA2 exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA2s, which have been already determined by x-ray and NMR analyses. Furthermore, the coordination geometry of the calcium(II) ion apparently deviated from that of eukaryotic PLA2s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA2 seems to be conserved between prokaryotic and eukaryotic cells. Demonstrating that the overall structure determined by x-ray analysis is almost the same as that determined by NMR analysis is useful to discuss the catalytic mechanism at the molecular level of the bacterial PLA2.