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PDBsum entry 1df0
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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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Crystal structure of calpain reveals the structural basis for ca(2+)-Dependent protease activity and a novel mode of enzyme activation.
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Authors
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C.M.Hosfield,
J.S.Elce,
P.L.Davies,
Z.Jia.
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Ref.
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EMBO J, 1999,
18,
6880-6889.
[DOI no: ]
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PubMed id
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Abstract
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The combination of thiol protease activity and calmodulin-like EF-hands is a
feature unique to the calpains. The regulatory mechanisms governing calpain
activity are complex, and the nature of the Ca(2+)-induced switch between
inactive and active forms has remained elusive in the absence of structural
information. We describe here the 2.6 A crystal structure of m-calpain in the
Ca(2+)-free form, which illustrates the structural basis for the inactivity of
calpain in the absence of Ca(2+). It also reveals an unusual thiol protease
fold, which is associated with Ca(2+)-binding domains through heterodimerization
and a C(2)-like beta-sandwich domain. Strikingly, the structure shows that the
catalytic triad is not assembled, indicating that Ca(2+)-binding must induce
conformational changes that re-orient the protease domains to form a functional
active site. The alpha-helical N-terminal anchor of the catalytic subunit does
not occupy the active site but inhibits its assembly and regulates
Ca(2+)-sensitivity through association with the regulatory subunit. This
Ca(2+)-dependent activation mechanism is clearly distinct from those of
classical proteases.
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Figure 3.
Figure 3 Calpain has a unique N-terminal anchor. (A) The helical
anchor (residues 2 -16 are shown) makes contacts only with D-VI
(colors as in Figure 1). (B) View down the helical axis
highlights interactions between the residues in the anchor
(magenta type) and D-VI (black type), represented as an
electrostatic GRASP surface (Nicholls et al., 1991) (red,
acidic; blue, basic). (C) Side view of (B) illustrates the depth
of the hydrophobic pocket in D-VI, which interacts with
hydrophobic residues Ala2, Gly3, Ile4, Ala5, Leu8 and Ala9 of
the anchor. This anchor inhibits active site assembly by
associating with the regulatory subunit, thus restricting
flexibility of protease D-I. The anchor also acts as a
co-chaperone in concert with D-VI, ensuring proper folding of
the catalytic subunit. (B) and (C) were created with the program
GRASP (Nicholls et al., 1991).
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Figure 4.
Figure 4 Domain III shares similar characteristics with a C[2]
domain. A typical C[2] domain exists as an anti-parallel  -sandwich
with several acidic residues at one end that form a binding
cradle for Ca^2+. The first C[2] domain from synaptotagmin
(cyan, PDB accession code 1RSY) (Sutton et al., 1995) and D-III
(green) have approximately the same overall dimensions, though
slightly differing topologies. Numerous acidic residues (red)
result in a highly negative potential, which is partially
stabilized by adjacent basic residues (blue).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
6880-6889)
copyright 1999.
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Secondary reference #1
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Title
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Structure of a calpain ca(2+)-Binding domain reveals a novel ef-Hand and ca(2+)-Induced conformational changes.
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Authors
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H.Blanchard,
P.Grochulski,
Y.Li,
J.S.Arthur,
P.L.Davies,
J.S.Elce,
M.Cygler.
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Ref.
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Nat Struct Biol, 1997,
4,
532-538.
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PubMed id
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Secondary reference #2
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Title
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Crystal structure of calcium bound domain VI of calpain at 1.9 a resolution and its role in enzyme assembly, Regulation, And inhibitor binding.
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Authors
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G.D.Lin,
D.Chattopadhyay,
M.Maki,
K.K.Wang,
M.Carson,
L.Jin,
P.W.Yuen,
E.Takano,
M.Hatanaka,
L.J.Delucas,
S.V.Narayana.
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Ref.
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Nat Struct Biol, 1997,
4,
539-547.
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PubMed id
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Secondary reference #3
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Title
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Crystallization and X-Ray crystallographic analysis of m-Calpain, A ca2+-Dependent protease.
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Authors
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C.M.Hosfield,
Q.Ye,
J.S.Arthur,
C.Hegadorn,
D.E.Croall,
J.S.Elce,
Z.Jia.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1999,
55,
1484-1486.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 P1 crystal of C105S-m-calpain. The approximate size is
0.2 × 0.2 × 0.2 mm.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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