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PDBsum entry 2zyk
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Sugar binding protein
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PDB id
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2zyk
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Sugar binding protein
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Title:
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Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin
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Structure:
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Solute-binding protein. Chain: a, b, c, d. Fragment: residues 1-397. Synonym: cyclodextrin-binding protein. Engineered: yes
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Source:
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Thermoactinomyces vulgaris. Organism_taxid: 2026. Strain: r-47. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Resolution:
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2.50Å
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R-factor:
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0.222
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R-free:
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0.285
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Authors:
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T.Tonozuka,A.Sogawa,M.Yamada,N.Matsumoto,H.Yoshida,S.Kamitori, K.Ichikawa,M.Mizuno,A.Nishikawa,Y.Sakano
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Key ref:
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T.Tonozuka
et al.
(2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
Febs J,
274,
2109-2120.
PubMed id:
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Date:
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26-Jan-09
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Release date:
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10-Feb-09
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Supersedes:
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PROCHECK
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Headers
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References
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Q9AJF5
(Q9AJF5_THEVU) -
Maltodextrin-binding protein from Thermoactinomyces vulgaris
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Seq:
Struc:
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417 a.a.
381 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Febs J
274:2109-2120
(2007)
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PubMed id:
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Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
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T.Tonozuka,
A.Sogawa,
M.Yamada,
N.Matsumoto,
H.Yoshida,
S.Kamitori,
K.Ichikawa,
M.Mizuno,
A.Nishikawa,
Y.Sakano.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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Mol Microbiol,
77,
183-199.
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PDB codes:
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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.
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FEBS J,
276,
3008-3019.
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PDB codes:
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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.
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J Biol Chem,
283,
13165-13173.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
