2ZYK

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

Replaces:  2DFZ

Summary for 2ZYK

• Entry DOI: 10.2210/pdb2zyk/pdb
• Related PRD ID: PRD_900042
• Descriptor: Solute-binding protein, Cyclooctakis-(1-4)-(alpha-D-glucopyranose) (3 entities in total)
• Functional Keywords: solute-binding protein, closed form, sugar binding protein
• Biological source: Thermoactinomyces vulgaris
• Total number of polymer chains: 4
• Total formula weight: 180008.02

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 citation

Tonozuka, 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

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

Experimental method

X-RAY DIFFRACTION (2.5 Å)