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PDBsum entry 1vff
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References listed in PDB file
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Key reference
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Title
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X-Ray structure of a membrane-Bound beta-Glycosidase from the hyperthermophilic archaeon pyrococcus horikoshii.
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Authors
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T.Akiba,
M.Nishio,
I.Matsui,
K.Harata.
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Ref.
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Proteins, 2004,
57,
422-431.
[DOI no: ]
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PubMed id
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Abstract
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The beta-glycosidase of the hyperthermophilic Archaeon Pyrococcus horikoshii is
a membrane-bound enzyme with the preferred substrate of alkyl-beta-glycosides.
In this study, the unusual structural features that confer the extreme
thermostability and substrate preferences of this enzyme were investigated by
X-ray crystallography and docking simulation. The enzyme was crystallized in the
presence of a neutral surfactant, and the crystal structure was solved by the
molecular replacement method and refined at 2.5 A. The main-chain fold of the
enzyme belongs to the (betaalpha)8 barrel structure common to the Family 1
glycosyl hydrolases. The active site is located at the center of the C-termini
of the barrel beta-strands. The deep pocket of the active site accepts one sugar
unit, and a hydrophobic channel extending radially from there binds the nonsugar
moiety of the substrate. The docking simulation for oligosaccharides and
alkylglucosides indicated that alkylglucosides with a long aliphatic chain are
easily accommodated in the hydrophobic channel. This sparingly soluble enzyme
has a cluster of hydrophobic residues on its surface, situated at the distal end
of the active site channel and surrounded by a large patch of positively charged
residues. We propose that this hydrophobic region can be inserted into the
membrane while the surrounding positively charged residues make favorable
contacts with phosphate groups on the inner surface of the membrane. The enzyme
could thus adhere to the membrane in the proximity of its glycolipid substrate.
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Figure 2.
Figure 2. Stereo view of the ribbon model of the BGPh
structure. The  -strands
and  -helices
of the ( )[8]
barrel core are numbered. The model is viewed along the axis of
the barrel. The N- and C-terminal ends are denoted by N and C,
respectively. -Helices,
-strands,
and loops are colored in red, dark blue, and yellow,
respectively.
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Figure 7.
Figure 7. Surface properties of the BGPh molecule and a
proposed model of its membrane bound form. (a) Arrangement of
amino acid residues on the surface are depicted as follows:
hydrophobic (white), aromatic (pink), basic (blue), acidic
(red), and polar neutral residues (green). (b) The electrostatic
potential mapped on the molecular surface; positive is in blue
and negative in red. (c) Ribbon model of the protein in the same
orientation as (a) and (b) for helping the reader to locate
these features in the structure. The active center is indicated
by arrows; the hydrophobic mound is encircled by a solid line.
The electrostatic potential map was obtained with DelPhi[42]
module of Insight II package. (d) Proposed model of BGPh bound
to the inner surface of the cell membrane. The protein molecule
is in the molecular surface model showing the calculated
electrostatic potential. The CPK model of dodecyl- -glucoside
is placed in the active site channel of BGPh. The membrane is
modeled by an array of CPK models of glucosyl caldarchaetidic
acid and glucosyl archaeol according to De Rosa et al.[26] The
thickness of the membrane is 55 Å in the model, but it
should be thinner in live Archaea due to the disordering of core
isoprenoid chains.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2004,
57,
422-431)
copyright 2004.
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