 |
PDBsum entry 1u4z
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Visualizing complexes of phospholipids with streptomyces phospholipase d by automated docking.
|
|
|
Authors
|
|
C.L.Aikens,
A.Laederach,
P.J.Reilly.
|
|
|
Ref.
|
|
Proteins, 2004,
57,
27-35.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
The first crystal structure of a phospholipase d.
|
|
|
Authors
|
|
I.Leiros,
F.Secundo,
C.Zambonelli,
S.Servi,
E.Hough.
|
|
|
Ref.
|
|
Structure, 2000,
8,
655-667.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Figure 2. Topology and tertiary structure of PLD. (a)
Overall topology of PLD from Streptomyces sp. strain PMF.
Modified figure from TOPS [46]. The N-terminal 260 residues are
shown in light blue and the remainder of the protein is colored
in dark blue, in order to separate the two domains. (b)
Stereographic overview of the tertiary arrangement of the
protein. Helices are shown in red and strands in yellow. The
protein is viewed from the outer membrane, and the
active-site-bound phosphate can be seen in the center of the
protein. This Figure was created using BOBSCRIPT. (c)
Stereographic presentation of the Ca trace of PLD, made using
BOBSCRIPT. The orientation of the protein is as in (b).
|
|
|
|
|
|
The above figure is
reproduced from the cited reference
with permission from Cell Press
|
|
|
|
|
|
|
