PDBsum entry 1kp4

Hydrolase

PDB id: 1kp4

Contents

Protein chain

122 a.a. *

Metals

_CA

Waters ×88

* Residue conservation analysis

PDB id:

1kp4

Name:

Hydrolase

Title:

Calcium-bound form of prokaryotic phospholipase a2

Structure:

Phospholipase a2. Chain: a. Engineered: yes

Source:

Streptomyces violaceoruber. Organism_taxid: 1935. Expressed in: streptomyces lividans tk24. Expression_system_taxid: 457428.

Resolution:

1.60Å R-factor: 0.150

Authors:

Y.Matoba,Y.Katsube,M.Sugiyama

Key ref:

Y.Matoba et al. (2002). The crystal structure of prokaryotic phospholipase A2. J Biol Chem, 277, 20059-20069. PubMed id: 11897785 DOI: 10.1074/jbc.M200263200

Date:

28-Dec-01 Release date: 04-Sep-02

Protein chain

Q6UV28  (Q6UV28_STRVN) -  Phospholipase A2 from Streptomyces violaceoruber

Seq: 150 a.a.

Struc: 122 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.4 - phospholipase A2.
• Reaction: a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H⁺
• Cofactor: Ca(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M200263200

J Biol Chem 277:20059-20069 (2002)

PubMed id: 11897785

The crystal structure of prokaryotic phospholipase A2.

Y.Matoba, Y.Katsube, M.Sugiyama.

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).

Selected figure(s)

Figure 5.
Fig. 5. Stereoviews of the catalytic site and surrounding hydrogen-bonding network. a and b, the calcium-free and calcium-bound forms of the S. violaceoruver PLA[2], respectively; c, N. naja atra PLA[2] (7). The hydrogen bonds are shown by black broken lines. The numbers in b and c show the distance (Å) between calcium(II) ion and the His64 N 1 (the His48 N 1 in N. naja atra).

Figure 6.
Fig. 6. Stereoviews of the calcium-binding site. a and b, the calcium-free and calcium-bound forms of the S. violaceoruver PLA[2], respectively; c, N. naja atra PLA[2] (7). A green ball represents the calcium(II) ion. The hydrogen bonds and coordination bonds to the calcium (II) ion are shown by black broken lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 20059-20069) copyright 2002.

Figures were selected by an automated process.