1KP4

CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2

Summary for 1KP4

• Entry DOI: 10.2210/pdb1kp4/pdb
• Related: 1FAZ 1IT4 1IT5
• Descriptor: phospholipase A2, CALCIUM ION (3 entities in total)
• Functional Keywords: phospholipase a2, prokaryote, calcium ion, hydrolase
• Biological source: Streptomyces violaceoruber
• Total number of polymer chains: 1
• Total formula weight: 13610.86

Authors

Matoba, Y.,Katsube, Y.,Sugiyama, M. (deposition date: 2001-12-28, release date: 2002-09-04, Last modification date: 2024-10-23)

Primary citation

Matoba, Y.,Katsube, Y.,Sugiyama, M.
The crystal structure of prokaryotic phospholipase A2.
J.Biol.Chem., 277:20059-20069, 2002

PubMed Abstract: In this study, the x-ray crystal structures of the calcium-free and calcium-bound forms of phospholipase A(2) (PLA(2)), 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-A resolution and an R-factor of 15.0% at a 1.6-A resolution, respectively. The overall structure of the prokaryotic PLA(2) exhibits a novel folding topology that demonstrates that it is completely distinct from those of eukaryotic PLA(2)s, 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 PLA(2)s. Regardless of the evolutionary divergence, the catalytic mechanism including the calcium(II) ion on secreted PLA(2) 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 PLA(2).

PubMed: 11897785
DOI: 10.1074/jbc.M200263200

Experimental method

X-RAY DIFFRACTION (1.6 Å)