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PDBsum entry 1kp4
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The crystal structure of prokaryotic phospholipase a2.
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Authors
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Y.Matoba,
Y.Katsube,
M.Sugiyama.
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Ref.
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J Biol Chem, 2002,
277,
20059-20069.
[DOI no: ]
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PubMed id
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Abstract
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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).
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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).
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
20059-20069)
copyright 2002.
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Secondary reference #1
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Title
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A novel prokaryotic phospholipase a2. Characterization, Gene cloning, And solution structure.
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Authors
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M.Sugiyama,
K.Ohtani,
M.Izuhara,
T.Koike,
K.Suzuki,
S.Imamura,
H.Misaki.
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Ref.
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J Biol Chem, 2002,
277,
20051-20058.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Hydrolysis of the 2-acyl ester bond of
1,2-diacylglycero-3-phosphocholine by PLA[2].
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Figure 8.
Fig. 8. Stereoview (a) and geometry change (b) of the
calcium-binding site in the S. violaceoruber PLA[2]. The
calcium-free and calcium-bound forms are displayed in yellow and
cyan, respectively. The calcium(II) ion is shown as a red ball.
The N-terminal Ala residue in the mature PLA[2] is numbered as 1.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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