2ZYN

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

Summary for 2ZYN

• Entry DOI: 10.2210/pdb2zyn/pdb
• Related: 2ZYK 2ZYM 2ZYO
• Related PRD ID: PRD_900012
• Descriptor: Solute-binding protein, Cycloheptakis-(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: 1
• Total formula weight: 44839.86

Authors

Matsumoto, M.,Yamada, M.,Kurakata, Y.,Yoshida, H.,Kamitori, S.,Nishikawa, A.,Tonozuka, T. (deposition date: 2009-01-27, release date: 2009-03-31, Last modification date: 2023-11-01)

Primary citation

Matsumoto, N.,Yamada, M.,Kurakata, Y.,Yoshida, H.,Kamitori, S.,Nishikawa, A.,Tonozuka, T.
Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein
Febs J., 276:3008-3019, 2009

PubMed Abstract: The crystal structures of Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein (TvuCMBP) complexed with alpha-cyclodextrin (alpha-CD), beta-cyclodextrin (beta-CD) and maltotetraose (G4) have been determined. A common functional conformational change among all solute-binding proteins involves switching from an open form to a closed form, which facilitates transporter binding. Escherichia coli maltodextrin-binding protein (EcoMBP), which is structurally homologous to TvuCMBP, has been determined to adopt the open form when complexed with beta-CD and the closed form when bound to G4. Here, we show that, unlike EcoMBP, TvuCMBP-alpha-CD and TvuCMBP-beta-CD adopt the closed form when complexed, whereas TvuCMBP-G4 adopts the open form. Only two glucose residues are evident in the TvuCMBP-G4 structure, and these bind to the C-domain of TvuCMBP in a manner similar to the way in which maltose binds to the C-domain of EcoMBP. The superposition of TvuCMBP-alpha-CD, TvuCMBP-beta-CD and TvuCMBP-gamma-CD shows that the positions and the orientations of three glucose residues in the cyclodextrin molecules overlay remarkably well. In addition, most of the amino acid residues interacting with these three glucose residues also participate in interactions with the two glucose residues in TvuCMBP-G4, regardless of whether the protein is in the closed or open form. Our results suggest that the mechanisms by which TvuCMBP changes from the open to the closed conformation and maintains the closed form appear to be different from those of EcoMBP, despite the fact that the amino acid residues responsible for the initial binding of the ligands are well conserved between TvuCMBP and EcoMBP.

PubMed: 19490104
DOI: 10.1111/j.1742-4658.2009.07020.x

Experimental method

X-RAY DIFFRACTION (1.7 Å)