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PDBsum entry 1fb2
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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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Regulation of catalytic function by molecular association: structure of phospholipase a2 from daboia russelli pulchella (dpla2) at 1.9 a resolution.
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Authors
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V.Chandra,
P.Kaur,
J.Jasti,
C.Betzel,
T.P.Singh.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1793-1798.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of phospholipase A(2) from the venom of Daboia russelli
pulchella has been refined to an R factor of 0.216 using 17,922 reflections to
1.9 A resolution. The structure contains two crystallographically independent
molecules in the asymmetric unit. The overall conformations of the two molecules
are essentially the same except for three regions, namely the calcium-binding
loop including Trp31, the beta-wing and the C-terminal residues 119-131.
Although these differences have apparently been caused by molecular packing,
they seem to have functional relevance. Particularly noteworthy is the
conformation of Trp31, which is favourable for substrate binding in one molecule
as it is aligned with one of the side walls of the hydrophobic channel, whereas
in the other molecule it is located at the mouth of the channel, thereby
blocking the entry of substrates leading to loss of activity. This feature is
unique to the present structure and does not occur in the dimers and trimers of
other PLA(2)s.
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Figure 1.
Figure 1 A region of the final 2F[o] - F[c] electron-density map
contoured at 1.5  and
the corresponding refined model. The diagram was produced using
the program O (Jones et al., 1991[Jones, T. A., Zou, J., Cowan,
S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.]).
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Figure 8.
Figure 8 Positioning of Trp31 vis-à-vis the hydrophobic binding
channel. The placement of Trp31 in molecule B (blue) reduces the
width of the channel, thus impairing its binding capability
while the corresponding width in molecule A (green) is optimum.
The distances between the two nearest atoms of Leu2 and Trp31
are 8.3 and 4.7 Å in molecules A and B, respectively.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
1793-1798)
copyright 2001.
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Secondary reference #1
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Title
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Three-Dimensional structure of a presynaptic neurotoxic phospholipase a2 from daboia russelli pulchella at 2.4 a resolution.
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Authors
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V.Chandra,
P.Kaur,
A.Srinivasan,
T.P.Singh.
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Ref.
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J Mol Biol, 2000,
296,
1117-1126.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. (a) Superimposition of C^α traces of DPLA[2]
(thick lines) and VPLA[2] (thin lines). The r.m.s. difference
for the C^α atoms is 1.2 Å. The corresponding shifts for
the neurotoxic (55–61 and 85–94), and anticoagulant
(53–77) fragments are 1.8 Å and 1.3 Å,
respectively. (b) Protruding side-chains of basic residues for
the anticoagulant site.
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Figure 4.
Figure 4. (a) The association of molecules A and B showing a
number of residues from both the molecules (black) and solvent
molecules (red) involved in the interactions between two
molecules: molecule A, Leu2, Leu17, Ala18, Ile19, Pro20, Trp31,
Arg43, Phe46, Ser70, Arg72, Met118, Leu119 and Asp122; molecule
B, Thr36, Ala40, Arg43, Phe46, Val47, Asn54, Glu97, Lys100,
Ile104, Gln108, Asn111, Leu130, Lys131 and Cys133 and 31 solvent
molecules. (b) Spatially two adjacent fragments 55–61 and
85–94. The segment 55–61 forms a β-turn I with a hydrogen
bond between Leu55 (O) and Cys61 (N). A tight loop, 85-94, is
stabilized by a number of intra-loop hydrogen bonds which are
indicated by dotted lines. The inter-segmental hydrogen bonds
(red, broken lines) are also indicated.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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