|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
Structures of the catalytic site mutants d99a and h48q and the calcium-Loop mutant d49e of phospholipase a2.
|
|
|
Authors
|
|
K.Sekar,
R.Biswas,
Y.Li,
M.Tsai,
M.Sundaralingam.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1999,
55,
443-447.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
0%.
|
|
|
|
Abstract
|
|
|
Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop
mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A
resolution. The D99A mutant is isomorphous to the orthorhombic recombinant
enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are
isomorphous to the trigonal recombinant enzyme, space group P3121. The two
active-site mutants show no major structural perturbations. The structural water
is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In
H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the
second water found in native His48 is absent. In the calcium-loop mutant D49E,
the two water molecules forming the pentagonal bipyramid around calcium are
absent and only one O atom of the Glu49 carboxylate group is coordinated to
calcium, resulting in only four ligands.
|
|
|
|
|
|
|
|
Figure 3.
Figure 3 The same stereoview of the calcium coordination in (a)
the mutant D49E and (b) in the trigonal recombinant PLA2 (Sekar
et al., 1998[Sekar, K., Sekharudu, Y. C., Tsai, M.-D. &
Sundaralingam, M. (1998). Acta Cryst. D54, 342-346.]). The
calcium ion is shown as a solid circle. The equatorial calcium
water W5 and the axial calcium water W12 are missing in the
mutant and are shown as open circles. In the mutant, only one of
the carboxylate O atoms is liganded to calcium, compared with
the recombinant enzyme where Asp49 forms a bidentate ligation.
Thus, calcium has only four ligands in the mutant while it has
seven ligands in the recombinant enzyme.
|
|
Figure 4.
Figure 4 The omit electron density of the mutated residue Glu49
and the calcium ion. Contours are shown at the 1.0  level.
Note that there are only four ligands around the calcium ion.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
443-447)
copyright 1999.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
High-Resolution refinement of orthorhombic bovine pancreatic phospholipase a2.
|
|
|
Authors
|
|
K.Sekar,
M.Sundaralingam.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1999,
55,
46-50.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
79%.
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Figure 2 A stereoview of (a) the omit electron-density map
showing the ordered surface-loop residues 60-70 in the present
orthorhombic form, contoured at the 1.0  level,
and (b) the water molecules (open circles) involved in hydrogen
bonding with the polar atoms of the surface-loop residues
produced using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P.
J. (1991). J. Appl. Cryst. 24, 946-950.]).
|
|
Figure 4.
Figure 4 A stereoview of the hydrogen-bonding (dashed lines)
network connecting the active/catalytic site and the calcium
coordination sphere. The omit electron-density map shows the
five water molecules commonly found in the active site: the
structural water (W11), the two calcium-coordinated waters (W5
and W12), the catalytic water (W6) and the second water (W7).
Contours are shown at the 1.0 level.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from the IUCr
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Structure of the complex of bovine pancreatic phospholipase a2 with a transition-State analogue.
|
|
|
Authors
|
|
K.Sekar,
A.Kumar,
X.Liu,
M.D.Tsai,
M.H.Gelb,
M.Sundaralingam.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1998,
54,
334-341.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 3.
Figure 3 (a) A stereoview of the recombinant bovine PLA2 enzyme
showing the active-site cleft and the inhibitor TSA (ball and
stick). Calcium ion is shown as grey circle and the disulfide
bonds are shown. (b) The above view has been rotated (rotation
-115° in y and -30° in x), which shows the atoms of the TSA
inhibitor in the active site. Note the calcium-binding loop is
above the inhibitor. The figures were produced using the program
MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst.
24, 946-950.]).
|
|
Figure 6.
Figure 6 (a) A stereoview of the free PLA2 structure showing the
two water molecules (W5 and W12) in the calcium coordination,
the structural water (W11) and the two waters (W6 and W7)
hydrogen bonded to N [122][delta] 1 and lying on either side of
the imidazole plane of His48. (b) Stereoview of the TSA complex
showing that the water molecules (W5, W6 and W12) are replaced
by the inhibitor phosphate/phosphonate anionic O atoms while W7
is dislodged by the close approach of the C3 atom of the
inhibitor. The structural water is retained in the present
PLA2-TSA complex.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from the IUCr
|
|
|
Secondary reference #3
|
|
|
Title
|
|
1.72 a resolution refinement of the trigonal form of bovine pancreatic phospholipase a2.
|
|
|
Authors
|
|
K.Sekar,
C.Sekharudu,
M.D.Tsai,
M.Sundaralingam.
|
|
|
Ref.
|
|
Acta Crystallogr D Biol Crystallogr, 1998,
54,
342-346.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
Figure 3.
Figure 3 A stereoview showing the hydrogen-bonding network of
the elongated active site.
|
|
|
|
|
|
The above figure is
reproduced from the cited reference
with permission from the IUCr
|
|
|
Secondary reference #4
|
|
|
Title
|
|
Crystal structure of the complex of bovine pancreatic phospholipase a2 with the inhibitor 1-Hexadecyl-3-(Trifluoroethyl)-Sn-Glycero-2-Phosphomethanol,.
|
|
|
Authors
|
|
K.Sekar,
S.Eswaramoorthy,
M.K.Jain,
M.Sundaralingam.
|
|
|
Ref.
|
|
Biochemistry, 1997,
36,
14186-14191.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #5
|
|
|
Title
|
|
Phospholipase a2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99.
|
|
|
Authors
|
|
K.Sekar,
B.Z.Yu,
J.Rogers,
J.Lutton,
X.Liu,
X.Chen,
M.D.Tsai,
M.K.Jain,
M.Sundaralingam.
|
|
|
Ref.
|
|
Biochemistry, 1997,
36,
3104-3114.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #6
|
|
|
Title
|
|
Phospholipase a2 engineering. Deletion of the c-Terminus segment changes substrate specificity and uncouples calcium and substrate binding at the zwitterionic interface.
|
|
|
Authors
|
|
B.Huang,
B.Z.Yu,
J.Rogers,
I.J.Byeon,
K.Sekar,
X.Chen,
M.Sundaralingam,
M.D.Tsai,
M.K.Jain.
|
|
|
Ref.
|
|
Biochemistry, 1996,
35,
12164-12174.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #7
|
|
|
Title
|
|
Phospholipase a2 engineering. X-Ray structural and functional evidence for the interaction of lysine-56 with substrates.
|
|
|
Authors
|
|
J.P.Noel,
C.A.Bingman,
T.L.Deng,
C.M.Dupureur,
K.J.Hamilton,
R.T.Jiang,
J.G.Kwak,
C.Sekharudu,
M.Sundaralingam,
M.D.Tsai.
|
|
|
Ref.
|
|
Biochemistry, 1991,
30,
11801-11811.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
