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PDBsum entry 2bgo
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Carbohydrate binding protein
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PDB id
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2bgo
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References listed in PDB file
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Key reference
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Title
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Structure of a mannan-Specific family 35 carbohydrate-Binding module: evidence for significant conformational changes upon ligand binding.
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Authors
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R.B.Tunnicliffe,
D.N.Bolam,
G.Pell,
H.J.Gilbert,
M.P.Williamson.
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Ref.
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J Mol Biol, 2005,
347,
287-296.
[DOI no: ]
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PubMed id
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Abstract
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Enzymes that digest plant cell wall polysaccharides generally contain
non-catalytic, carbohydrate-binding modules (CBMs) that function by attaching
the enzyme to the substrate, potentiating catalytic activity. Here, we present
the first structure of a family 35 CBM, derived from the Cellvibrio japonicus
beta-1,4-mannanase Man5C. The NMR structure has been determined for both the
free protein and the protein bound to mannopentaose. The data show that the
protein displays a typical beta-jelly-roll fold. Ligand binding is not located
on the concave surface of the protein, as occurs in many CBMs that display the
jelly-roll fold, but is formed by the loops that link the two beta-sheets of the
protein, similar to family 6 CBMs. In contrast to the majority of CBMs, which
are generally rigid proteins, CBM35 undergoes significant conformational change
upon ligand binding. The curvature of the binding site and the narrow binding
cleft are likely to be the main determinants of binding specificity. The
predicted solvent exposure of O6 at several subsites provides an explanation for
the observed accommodation of decorated mannans. Two of the key aromatic
residues in Man5C-CBM35 that interact with mannopentaose are conserved in
mannanase-derived CBM35s, which will guide specificity predictions based on the
primary sequence of proteins in this CBM family.
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Figure 2.
Figure 2. Stereo rainbow representations of the backbone
atoms (N, C^a, C') of 20 structure ensembles of (a) free
Man5C-CBM35 and (c) mannopentaose bound. Cartoon representation
of the fold of (b) free and (d) bound protein are shown on the
right, showing the b-sandwich fold maintained in both states.
(b) and (d) Strands are numbered and the helical turn is
highlighted in red. All protein images were produced in Pymol
(DeLano Scientific; http://www.pymol.org).
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Figure 7.
Figure 7. Overlay of the bound structure of Man5C-CBM35
(green) with the xylan-binding CtCBM625 (PDB 1gmm) (blue). The
aromatics involved in carbohydrate binding are shown in both
proteins with CBM6 binding clefts A and B highlighted. The
aromatics of CtCBM6 are coloured cyan and are (from left to
right) Tyr40, Tyr34 and Trp 92. The yellow aromatics of
Man5C-CBM35 are (left to right) Trp109, Tyr111 and Tyr60.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
347,
287-296)
copyright 2005.
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