PDBsum entry 1u4z

Hydrolase

PDB id: 1u4z

Contents

Protein chain

496 a.a.

Ligands

PX8

Theoretical model

PDB id:

1u4z

Name:

Hydrolase

Title:

Ligand px8 docked to phospholipase d (1f0i)

Structure:

Phospholipase d. Chain: a. Ec: 3.1.4.4

Source:

Streptomyces sp.. Bacteria. Strain: pmf

Authors:

C.L.Aikens,A.T.Laederach,P.J.Reilly

Key ref:

C.L.Aikens et al. (2004). Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking. Proteins, 57, 27-35. PubMed id: 15326592 DOI: 10.1002/prot.20180

Date:

26-Jul-04 Release date: 05-Jul-05

Protein chain

No UniProt id for this chain

Struc: 496 a.a.

DOI no: 10.1002/prot.20180

Proteins 57:27-35 (2004)

PubMed id: 15326592

Visualizing complexes of phospholipids with Streptomyces phospholipase D by automated docking.

C.L.Aikens, A.Laederach, P.J.Reilly.

ABSTRACT

The automated docking program AutoDock was used to dock nine phosphatidic acids (PAs), six phosphatidylcholines, five phosphatidylethanolamines, four phosphatidylglycerols, one phosphatidylinositol and two phosphatidylserines, which have two identical saturated fatty acid residues with an even numbers of carbon atoms, onto the active site of Streptomyces sp. PMF phospholipase D (PLD). Two PAs with one double bond on the fatty acid chain linked to the C2 of the glycerol residue were also docked. In general, binding energies become progressively more negative as fatty acid residues become longer. When these residues are of sufficient length, one is coiled against a hydrophobic cliff in a well that also holds the glycerol and phosphate residues and the head group, while the other generally is bound by a hydrophobic surface outside the well. Phosphatidylcholines have the only head group that is firmly bound by the active site, giving a possible structural explanation for the low selectivity of Streptomyces PLD for other phospholipid substrates.

Selected figure(s)

Figure 1.
Figure 1. Reactions catalyzed by PLD.

Figure 5.
Figure 5. Space-filling illustrations of the docking of (a) PA-14 and PA-14:1 and (b) PA-18 and PA-18:1 in the PLD active site. Hydrophobic (white), negatively-charged (red), and positively-charged (blue) surfaces. The positive surface at the center of the illustrations is composed of the putative catalytic residues His165 and His438, as well as Lys167 and Lys440. The hydrophobic cliff is at the bottom of the illustrations.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 57, 27-35) copyright 2004.

Figures were selected by an automated process.