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PDBsum entry 1nx2
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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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A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
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Authors
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B.Todd,
D.Moore,
C.C.Deivanayagam,
G.D.Lin,
D.Chattopadhyay,
M.Maki,
K.K.Wang,
S.V.Narayana.
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Ref.
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J Mol Biol, 2003,
328,
131-146.
[DOI no: ]
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PubMed id
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Abstract
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The Ca(2+)-dependent cysteine protease calpain along with its endogenous
inhibitor calpastatin is widely distributed. The interactions between calpain
and calpastatin have been studied to better understand the nature of calpain
inhibition by calpastatin, which can aid the design of small molecule inhibitors
to calpain. Here we present the crystal structure of a complex between a
calpastatin peptide and the calcium-binding domain VI of calpain. DIC19 is a 19
residue peptide, which corresponds to one of the three interacting domains of
calpastatin, which is known to interact with domain VI of calpain. We present
two crystal structures of DIC19 bound to domain VI of calpain, determined by
molecular replacement methods to 2.5A and 2.2A resolution. In the process of
crystallizing the inhibitor complex, a new native crystal form was identified
which had the homodimer 2-fold axis along a crystallographic axis as opposed to
the previously observed dimer in the asymmetric unit. The crystal structures of
the native domain VI and its inhibitor PD150606
(3-(4-iodophenyl)-2-mercapto-(Z)-2-propenoic acid) complex were determined with
the help of molecular replacement methods to 2.0A and 2.3A resolution,
respectively. In addition, we built a homology model for the complex between
domain IV and DIA19 peptide of calpastatin. Finally, we present a model for the
calpastatin-inhibited calpain.
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Figure 2.
Figure 2. Ribbon representation of the domain VI crystal
structure. (a) Stereographic Ribbon diagrams of the domain VI
monomer present in the asymmetric unit. The bound calcium atoms
are represented as silver colored spheres. Helices are labeled
according to their EF-hand numbering ranging from EF1 to EF5,
respectively. The bound DIC19 peptide in helical conformation is
represented in yellow and the "mysterious peptide" appeared in
the same location as observed in ALG-2 crystal structure[52.] is
presented in purple. (b) Ribbon representation of the DVI dimer,
depicting interactions through the crystallographic 2-fold axis.
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Figure 5.
Figure 5. Stereo view of the surface plots of the
hydrophobic inhibitor binding sites. (a) The DIC19 binding
region in calcium-bound DVI. DIC19, represented as a helical
segment, yellow in color, clearly displays its amphipathic
nature with its bulky hydrophobic side-chains buried deep into
DVI and polar residues exposed to the solvent (side-chains
removed for clarity). (b) Bulky hydrophobic ring of the
inhibitor PD150606 and Phe610 of DIC19 occupy the same region of
DVI. However, the hydrophobic region that accommodates these
inhibitor molecules seems to be flexible enough, varying in size
to accommodate different sized inhibitors. c) View of the
inhibitor binding regions in the calcium-free DVI structure.
DIC19 is positioned in the same place, as in previous Figures,
indicating the narrowness of the hydrophobic region.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
328,
131-146)
copyright 2003.
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