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PDBsum entry 2zyk
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Sugar binding protein
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PDB id
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2zyk
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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 basis for cyclodextrin recognition by thermoactinomyces vulgaris cyclo/maltodextrin-Binding protein.
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Authors
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T.Tonozuka,
A.Sogawa,
M.Yamada,
N.Matsumoto,
H.Yoshida,
S.Kamitori,
K.Ichikawa,
M.Mizuno,
A.Nishikawa,
Y.Sakano.
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Ref.
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Febs J, 2007,
274,
2109-2120.
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PubMed id
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Abstract
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The crystal structure of a Thermoactinomyces vulgaris cyclo/maltodextrin-binding
protein (TvuCMBP) complexed with gamma-cyclodextrin has been determined. Like
Escherichia coli maltodextrin-binding protein (EcoMBP) and other bacterial
sugar-binding proteins, TvuCMBP consists of two domains, an N- and a C-domain,
both of which are composed of a central beta-sheet surrounded by alpha-helices;
the domains are joined by a hinge region containing three segments.
gamma-Cyclodextrin is located at a cleft formed by the two domains. A common
functional conformational change has been reported in this protein family, which
involves switching from an open form to a sugar-transporter bindable form,
designated a closed form. The TvuCMBP-gamma-cyclodextrin complex structurally
resembles the closed form of EcoMBP, indicating that TvuCMBP complexed with
gamma-cyclodextrin adopts the closed form. The fluorescence measurements also
showed that the affinities of TvuCMBP for cyclodextrins were almost equal to
those for maltooligosaccharides. Despite having similar folds, the sugar-binding
site of the N-domain part of TvuCMBP and other bacterial sugar-binding proteins
are strikingly different. In TvuCMBP, the side-chain of Leu59 protrudes from the
N-domain part into the sugar-binding cleft and orients toward the central cavity
of gamma-cyclodextrin, thus Leu59 appears to play the key role in binding. The
cleft of the sugar-binding site of TvuCMBP is also wider than that of EcoMBP.
These findings suggest that the sugar-binding site of the N-domain part and the
wide cleft are critical in determining the specificity of TvuCMBP for
gamma-cyclodextrin.
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Secondary reference #1
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Title
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Crystal structures of open and closed forms of cyclo/maltodextrin-Binding protein.
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Authors
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N.Matsumoto,
M.Yamada,
Y.Kurakata,
H.Yoshida,
S.Kamitori,
A.Nishikawa,
T.Tonozuka.
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Ref.
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Febs J, 2009,
276,
3008-3019.
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PubMed id
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