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2ZYK

Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin

Replaces:  2DFZ
Summary for 2ZYK
Entry DOI10.2210/pdb2zyk/pdb
Related PRD IDPRD_900042
DescriptorSolute-binding protein, Cyclooctakis-(1-4)-(alpha-D-glucopyranose) (3 entities in total)
Functional Keywordssolute-binding protein, closed form, sugar binding protein
Biological sourceThermoactinomyces vulgaris
Total number of polymer chains4
Total formula weight180008.02
Authors
Tonozuka, T.,Sogawa, A.,Yamada, M.,Matsumoto, N.,Yoshida, H.,Kamitori, S.,Ichikawa, K.,Mizuno, M.,Nishikawa, A.,Sakano, Y. (deposition date: 2009-01-26, release date: 2009-02-10, Last modification date: 2024-04-03)
Primary citationTonozuka, T.,Sogawa, A.,Yamada, M.,Matsumoto, N.,Yoshida, H.,Kamitori, S.,Ichikawa, K.,Mizuno, M.,Nishikawa, A.,Sakano, Y.
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein
Febs J., 274:2109-2120, 2007
Cited by
PubMed Abstract: 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.
PubMed: 17371546
DOI: 10.1111/j.1742-4658.2007.05753.x
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.5 Å)
Structure validation

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