2zyk is a 4 chain structure with sequence from Atcc 43649. This structure supersedes the now removed PDB entry 2dfz. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.,Tonozuka T, Sogawa A, Yamada M, Matsumoto N, Yoshida H, Kamitori S, Ichikawa K, Mizuno M, Nishikawa A, Sakano Y FEBS J. 2007 Apr;274(8):2109-20. Epub 2007 Mar 20. PMID:17371546[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
↑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. 2007 Apr;274(8):2109-20. Epub 2007 Mar 20. PMID:17371546 doi:https://dx.doi.org/10.1111/j.1742-4658.2007.05753.x
