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PDBsum entry 2gdv
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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 rearrangements of sucrose phosphorylase from bifidobacterium adolescentis during sucrose conversion.
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Authors
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O.Mirza,
L.K.Skov,
D.Sprogøe,
L.A.Van den broek,
G.Beldman,
J.S.Kastrup,
M.Gajhede.
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Ref.
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J Biol Chem, 2006,
281,
35576-35584.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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The reaction mechanism of sucrose phosphorylase from Bifidobacterium
adolescentis (BiSP) was studied by site-directed mutagenesis and x-ray
crystallography. An inactive mutant of BiSP (E232Q) was co-crystallized with
sucrose. The structure revealed a substrate-binding mode comparable with that
seen in other related sucrose-acting enzymes. Wild-type BiSP was also
crystallized in the presence of sucrose. In the dimeric structure, a covalent
glucosyl intermediate was formed in one molecule of the BiSP dimer, and after
hydrolysis of the glucosyl intermediate, a beta-D-glucose product complex was
formed in the other molecule. Although the overall structure of the
BiSP-glucosyl intermediate complex is similar to that of the BiSP(E232Q)-sucrose
complex, the glucose complex discloses major differences in loop conformations.
Two loops (residues 336-344 and 132-137) in the proximity of the active site
move up to 16 and 4 A, respectively. On the basis of these findings, we have
suggested a reaction cycle that takes into account the large movements in the
active-site entrance loops.
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Figure 1.
FIGURE 1. Schematic representation of the domain
organization of the mixed dimer of BiSP. The glucosyl
intermediate (molecule A; left) and the glucose hydrolysis
product (molecule B; right) are shown as red spheres. domains A,
B, B', and C are colored green, yellow, blue, and orange,
respectively. N and C correspond to the N and C termini,
respectively, whereas A and B indicate the positions of loops A
and B.
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Figure 4.
FIGURE 4. Structural changes occurring during the enzyme
reaction. A, close-up view of loops A and B of the wild-type
BiSP covalent intermediate (molecule A; cyan) superimposed on
the glucose product-bound form (molecule B; yellow). The bound
glucose of molecule B is shown for clarity. B, close-up view of
loops A and B and the noncovalently bound glucose molecule of
the wild-type BiSP-glucose complex. Glucose 1-phosphate (yellow)
has been modeled based on the position of the glucose
interacting with Arg^135 and Tyr^344. C, proposed intermolecular
phosphate-binding site created by two Arg^135 residues. The
distances indicated by dashed lines are 3.9 Å. The bound
sucrose molecules are shown as red van der Waals spheres.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
35576-35584)
copyright 2006.
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