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PDBsum entry 3fii
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Hydrolase, toxin/protein transport
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PDB id
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3fii
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References listed in PDB file
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Key reference
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Title
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Mode of vamp substrate recognition and inhibition of clostridium botulinum neurotoxin f.
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Authors
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R.Agarwal,
J.J.Schmidt,
R.G.Stafford,
S.Swaminathan.
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Ref.
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Nat Struct Biol, 2009,
16,
789-794.
[DOI no: ]
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PubMed id
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Abstract
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Clostridium botulinum neurotoxins (BoNTs) cleave neuronal proteins responsible
for neurotransmitter release, causing the neuroparalytic disease botulism. BoNT
serotypes B, D, F and G cleave and inactivate vesicle-associated membrane
protein (VAMP), each at a unique peptide bond. The specificity of BoNTs depends
on the mode of substrate recognition. We have investigated the mechanism of
substrate recognition of BoNT F by determining the crystal structures of its
complex with two substrate-based inhibitors, VAMP 22-58/Gln58D-cysteine and
27-58/Gln58D-cysteine. The inhibitors bind to BoNT F in the canonical direction
(as seen for BoNTs A and E substrates) but are positioned specifically via three
major exosites away from the active site. The cysteine sulfur of the inhibitors
interacts with the zinc and exists as sulfinic acid in the inhibitor VAMP
27-58/Gln58D-cysteine. Arg133 and Arg171, which form part of two separate
exosites, are crucial for substrate binding and catalysis.
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Figure 2.
(a) Interactions of active site zinc with inh1 and inh2. BoNT
F residues in the BoNT F–inh1 and BoNT F–inh2 complexes,
D-Cys and D-Cys-sulfinic acid, are shown in cyan, light gray,
orange and green stick model, respectively. Whereas the sulfur
of D-Cys in inh1 has one interaction (2.52 Å with zinc,
red label), sulfur, OD1 and OD2 of D-Cys sulfinic acid in inh2
have many interactions with the enzyme molecule (blue labels).
(b) Interactions of inh1 at and near the BoNT F active site.
BoNT F is shown in ribbons (sky blue) and stick model (light
gray) and zinc is in sphere model (magenta), whereas inh1 is in
green stick model. BoNT F and VAMP residues are labeled in black
and blue, respectively. All interactions between BoNT F and VAMP
are shown using dashed lines.
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Figure 3.
VAMP inhibitor (inh1) is shown in the middle panel in colored
secondary-structure boxes (loop, yellow;  -strand,
cyan; helix, pink). On either side of the middle panel are the
enzyme residues (BoNT F–inh1). These interactions are equally
applicable for the common residues of inh1 and inh2 with minor
differences in distances, except for the interaction between
VAMP Asp40 and BoNT F Lys29, which is present only in inh2. The
color-coding for enzyme residues is based on their interaction
with the VAMP main chain (MC) or side chains (SC), and vice
versa. Colors for the VAMP–BoNT F interactions are: MC:SC,
pink; MC:MC, blue; SC:SC, cyan; SC:MC, brown. The intra-chain
interactions (in violet) of VAMP at exosite 1 have both MC:MC
and also hydrophobic SC:SC.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2009,
16,
789-794)
copyright 2009.
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