The Crystal Structure of Prokaryotic Phospholipase A2

• Published in: The Journal of biological chemistry 2002-05, Vol.277 (22), p.20059-20069
• Main Authors: Matoba, Yasuyuki, Katsube, Yukiteru, Sugiyama, Masanori
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Base Sequence; Binding Sites; Calcium - metabolism; Cloning, Molecular; Crystallography, X-Ray; Hydrogen Bonding; Hydrolysis; Ions; Kinetics; Magnetic Resonance Spectroscopy; Models, Chemical; Models, Molecular; Molecular Sequence Data; Phospholipases A - chemistry; Phospholipases A - physiology; Phospholipases A2; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Recombinant Proteins - chemistry; Streptomyces - enzymology
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M200263200

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.