 |
PDBsum entry 2fqv
|
|
|
|
References listed in PDB file
|
 |
|
Key reference
|
|
|
Title
|
|
A common allosteric site and mechanism in caspases.
|
|
|
Authors
|
|
J.M.Scheer,
M.J.Romanowski,
J.A.Wells.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2006,
103,
7595-7600.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
We present a common allosteric mechanism for control of inflammatory and
apoptotic caspases. Highly specific thiol-containing inhibitors of the human
inflammatory caspase-1 were identified by using disulfide trapping, a method for
site-directed small-molecule discovery. These compounds became trapped by
forming a disulfide bond with a cysteine residue in the cavity at the dimer
interface approximately 15 A away from the active site. Mutational and
structural analysis uncovered a linear circuit of functional residues that runs
from one active site through the allosteric cavity and into the second active
site. Kinetic analysis revealed robust positive cooperativity not seen in other
endopeptidases. Recently, disulfide trapping identified a similar small-molecule
site and allosteric transition in the apoptotic caspase-7 that shares only a 23%
sequence identity with caspase-1. Together, these studies show a general
small-molecule-binding site for functionally reversing the zymogen activation of
caspases and suggest a common regulatory site for the allosteric control of
inflammation and apoptosis.
|
|
|
|
|
|
|
|
Figure 1.
Fig. 1. Structure of an allosteric inhibitor bound to
caspase-1. (a) 2F[o] - F[c] electron density for Compound 34
used for compound model building, contoured at 1  , is
shown as a blue mesh at the dimer interface (PDB ID code 2FQQ).
(b) Two molecules of Compound 34 are shown as spheres in the
central cavity at the dimer interface of caspase-1. (c) Residues
involved in forming the binding pocket for Compound 34 are shown
as spheres. Residues from the large subunit (Glu-241, Gln-257,
and Arg-286) are colored blue, and residues from the small
subunit (Thr-388, Glu-390, and Arg-391) are colored tan. (d)
Residues likely involved in the mechanism of inhibition of
caspase-1 by allosteric compounds are displayed. Arg-286
adjacent to the catalytic Cys-285 is located >12 Å from
Glu-390, to which it is salt-bridged in the active conformation.
The amide nitrogen of the linker group of Compound 34 is within
a hydrogen-bonding distance of the Glu-390 carboxylate. Arg-391
is shown to indicate the boundary of the binding pocket.
|
|
Figure 3.
Fig. 3. Structural analysis of mutations in the allosteric
circuit of caspase-1. (a) A network of interactions across the
dimer interface of caspase-1 in the z-VAD-FMK-inhibited protein.
The inhibitor is shown as yellow sticks in the upper left and
lower right. The active-site Cys-285 and Arg-286 are displayed
as blue sticks, Glu-390 at the dimer interface as tan sticks,
and a water molecule mediating the interaction between the two
Glu residues is shown as a red sphere. (b) The x-ray crystal
structure of each allosteric-circuit mutant was determined in
the presence of the active-site inhibitor z-VAD-FMK. All
structures (PDB ID codes 2FQS, R286A; 2FQU, E390A; and 2FQV,
R286A/E390A) adopted a dimeric structure very similar to that of
the wild-type enzyme in complex with an active-site inhibitor
(PDB ID code 2FQR). No significant conformational changes were
observed in the enzymes except for those involving residues in
the allosteric circuit. The 2F[o] - F[c] electron density for
residues Arg-286, Glu-390, and Thr-388 is displayed. (Bottom
Left) The position of Compound 34 displayed as spheres. (Bottom
Right) The ligand-free (apo) conformation of caspase-1.
|
|
|
|
|
|
|
|
|
|
