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PDBsum entry 1v02
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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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Structural determinants of substrate specificity in family 1 beta-Glucosidases: novel insights from the crystal structure of sorghum dhurrinase-1, A plant beta-Glucosidase with strict specificity, In complex with its natural substrate.
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Authors
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L.Verdoucq,
J.Morinière,
D.R.Bevan,
A.Esen,
A.Vasella,
B.Henrissat,
M.Czjze.
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Ref.
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J Biol Chem, 2004,
279,
31796-31803.
[DOI no: ]
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PubMed id
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Abstract
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Plant beta-glucosidases play a crucial role in defense against pests. They
cleave, with variable specificity, beta-glucosides to release toxic aglycone
moieties. The Sorghum bicolor beta-glucosidase isoenzyme Dhr1 has a strict
specificity for its natural substrate dhurrin
(p-hydroxy-(S)-mandelonitrile-beta-D-glucoside), whereas its close homolog, the
maize beta-glucosidase isoenzyme Glu1, which shares 72% sequence identity,
hydrolyzes a broad spectrum of substrates in addition to its natural substrate
2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one. Structural
data from enzyme.substrate complexes of Dhr1 show that the mode of aglycone
binding differs from that previously observed in the homologous maize enzyme.
Specifically, the data suggest that Asn(259), Phe(261), and Ser(462), located in
the aglycone-binding site of S. bicolor Dhr1, are crucial for aglycone
recognition and binding. The tight binding of the aglycone moiety of dhurrin
promotes the stabilization of the reaction intermediate in which the glycone
moiety is in a deformed (1)S(3) conformation within the glycone-binding site,
ready for nucleophilic attack to occur. Compared with the broad specificity
maize beta-glucosidase, this different binding mode explains the narrow
specificity of sorghum dhurrinase-1.
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Figure 4.
FIG. 4. Dhurrin bound in the active sites to SbDhr1-E189D
and glucotetrazole bound to ZmGlu1-E191D. A, electron density
surrounding the dhurrin molecule in the active site of
SbDhr1-E189D. The 2F[o] - F[c] Fourier difference maps at the
final stage of refinement are shown contoured at 1  above
the mean density. B, a slice in the surface representation of
SbDhr1 in complex with dhurrin showing the cyano group-binding
pocket. The dipole moment of the polar pocket, calculated with
GRASP (28), coincides with that of the cyano group. C, electron
density around the glucotetrazole molecule in the active site of
ZmGlu1-E191D. The F[o] - F[c] Fourier difference maps before
refinement are shown, calculated using only the enzyme model
phases without substrate, contoured at 2.5 above the mean density.
D, superimposition of the active sites of myrosinase (blue) and
ZmGlu1 (yellow), both in complex with the glucotetrazole
inhibitor molecule.
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Figure 5.
FIG. 5. Superimposition of the glucose moieties of
DIMBOA-Glc in ZmGlu1 and dhurrin in SbDhr1. The glucose ring of
DIM-BOA-Glc has rotated by  60° with respect to
that of dhurrin. Consequently, the residues binding the sugar
groups O-2, O-3, and O-4 in dhurrin bind O-3, O-4, and O-6 in
DIMBOA-Glc. See also Table III. In each box, the top residue
occurs in ZmGlu1, and the bottom residue occurs in SbDhr1. Of
the 2 glutamates shown by stick representation, Glu464 occurs in
ZmGlu1, whereas Glu460 occurs in SbDhr1.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
31796-31803)
copyright 2004.
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