PDBsum entry 2dfz

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Sugar binding protein PDB id
Protein chains
381 a.a. *
Waters ×539
* Residue conservation analysis
Superseded by: 2zyk 2zyk
PDB id:
Name: Sugar binding protein
Title: Crystal structure of cyclodextrin-binding protein complexed with gamma-cyclodextrin
Structure: Periplasmic binding protein. Chain: a, b, c, d. Fragment: residues 17-397. Synonym: cyclo/maltodextrin-binding protein. Engineered: yes
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.50Å     R-factor:   0.218     R-free:   0.268
Authors: T.Tonozuka,A.Sogawa,M.Yamada,N.Matsumoto,H.Yoshida, S.Kamitori,K.Ichikawa,M.Mizuno,A.Nishikawa,Y.Sakano
Key ref: T.Tonozuka et al. (2007). Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein. FEBS J, 274, 2109-2120. PubMed id: 17371546
07-Mar-06     Release date:   06-Mar-07    
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Protein chains
No UniProt id for this chain
Struc: 381 a.a.
Key:    Secondary structure  CATH domain


FEBS J 274:2109-2120 (2007)
PubMed id: 17371546  
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
T.Tonozuka, A.Sogawa, M.Yamada, N.Matsumoto, H.Yoshida, S.Kamitori, K.Ichikawa, M.Mizuno, A.Nishikawa, Y.Sakano.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
19490104 N.Matsumoto, M.Yamada, Y.Kurakata, H.Yoshida, S.Kamitori, A.Nishikawa, and T.Tonozuka (2009).
Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein.
  FEBS J, 276, 3008-3019.
PDB codes: 2zym 2zyn 2zyo
18332142 R.Suzuki, J.Wada, T.Katayama, S.Fushinobu, T.Wakagi, H.Shoun, H.Sugimoto, A.Tanaka, H.Kumagai, H.Ashida, M.Kitaoka, and K.Yamamoto (2008).
Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.
  J Biol Chem, 283, 13165-13173.
PDB codes: 2z8d 2z8e 2z8f
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