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PDBsum entry 2d80
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References listed in PDB file
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Key reference
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Title
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The crystal structure of polyhydroxybutyrate depolymerase from penicillium funiculosum provides insights into the recognition and degradation of biopolyesters.
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Authors
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T.Hisano,
K.Kasuya,
Y.Tezuka,
N.Ishii,
T.Kobayashi,
M.Shiraki,
E.Oroudjev,
H.Hansma,
T.Iwata,
Y.Doi,
T.Saito,
K.Miki.
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Ref.
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J Mol Biol, 2006,
356,
993.
[DOI no: ]
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PubMed id
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Abstract
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Polyhydroxybutyrate is a microbial polyester that can be produced from renewable
resources, and is degraded by the enzyme polyhydroxybutyrate depolymerase. The
crystal structures of polyhydroxybutyrate depolymerase from Penicillium
funiculosum and its S39A mutant complexed with the methyl ester of a trimer
substrate of (R)-3-hydroxybutyrate have been determined at resolutions of 1.71A
and 1.66A, respectively. The enzyme is comprised of a single domain, which
represents a circularly permuted variant of the alpha/beta hydrolase fold. The
catalytic residues Ser39, Asp121, and His155 are located at topologically
conserved positions. The main chain amide groups of Ser40 and Cys250 form an
oxyanion hole. A crevice is formed on the surface of the enzyme, to which a
single polymer chain can be bound by predominantly hydrophobic interactions with
several hydrophobic residues. The structure of the S39A mutant-trimeric
substrate complex reveals that Trp307 is responsible for the recognition of the
ester group adjacent to the scissile group. It is also revealed that the
substrate-binding site includes at least three, and possibly four, subsites for
binding monomer units of polyester substrates. Thirteen hydrophobic residues,
which are exposed to solvent, are aligned around the mouth of the crevice,
forming a putative adsorption site for the polymer surface. These residues may
contribute to the sufficient binding affinity of the enzyme for PHB granules
without a distinct substrate-binding domain.
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Figure 4.
Figure 4. Simulated-annealing |mF[o] -DF[c]| electron
density map for H(R3HB)[3]M bound to the S39A mutant, calculated
from the model excluding H(R3HB)[3]M. Models of S39A and the
R3HB trimer (H(R3HB)[3]M lacking the methyl group) are also
shown as a line and a stick model, respectively. The map is
contoured at 3.5s. Figures were produced using the PyMOL program
(DeLano, W. L.; http://www.pymol.org/).
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Figure 5.
Figure 5. A close-up stereoview of the active site (the
S39A-H(R3HB)[3]M complex). Side-chains of catalytic residues and
residues forming the substrate-binding site in the crevice are
represented as ball-and-stick models. The amide nitrogen atoms
of Ser40, Cys250, and Asn302 are also shown. A model of the R3HB
trimer (designated as (R3HB)[3]) is also shown as a black
ball-and-stick model. A hydrogen bond between Nd1 atom of Trp307
and the carbonyl oxygen of an ester linkage adjacent to a
scissile linkage, and one between His155 and Asp121 are
indicated as green lines. The side-chain of Ser39 of the
wild-type protein (shown in red) is superimposed on Ala39 of the
mutant model, and a hydrogen bond between the Og atom of Ser39
and the amide group of Ser40 is tentatively indicated with a
green broken line.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
356,
993-0)
copyright 2006.
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