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PDBsum entry 1gmm
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The location of the ligand-Binding site of carbohydrate-Binding modules that have evolved from a common sequence is not conserved.
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Authors
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M.Czjzek,
D.N.Bolam,
A.Mosbah,
J.Allouch,
C.M.Fontes,
L.M.Ferreira,
O.Bornet,
V.Zamboni,
H.Darbon,
N.L.Smith,
G.W.Black,
B.Henrissat,
H.J.Gilbert.
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Ref.
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J Biol Chem, 2001,
276,
48580-48587.
[DOI no: ]
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PubMed id
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Abstract
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Polysaccharide-degrading enzymes are generally modular proteins that contain
non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity
of the catalytic module. CBMs have been grouped into sequence-based families,
and three-dimensional structural data are available for half of these families.
Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM
from family 6 (CBM6), for which no structural data are available. We have
determined the crystal structure of this module to a resolution of 2.1 A. The
protein is a beta-sandwich that contains two potential ligand-binding clefts
designated cleft A and B. The CBM interacts primarily with xylan, and NMR
spectroscopy coupled with site-directed mutagenesis identified cleft A,
containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall
fold of CBM6 is similar to proteins in CBM families 4 and 22, although
surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B
in CBM6. These structural data define a superfamily of CBMs, comprising CBM4,
CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a
relatively small number of ancestors, the structural elements involved in ligand
recognition have been assembled at different locations on the ancestral scaffold.
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Figure 1.
Fig. 1. Electron density map at 2.1 Å and the final
structural model represented as sticks. a, final electron
density map, contoured at a 1  level, in
the region of Tyr-34 and Trp-92, also showing the putative
sodium ion. b, electron density map (1 level)
showing the presence of a structural calcium ion bridging the N-
and C-terminal ends. The figures were produced using the program
TURBO-FRODO (26).
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Figure 2.
Fig. 2. Ribbon and surface representations of CBM6. a,
view showing the ligand-binding cleft (cleft A) formed by the
loops between the two  -sheets of
the sandwich fold. b, surface representation of CBM6 in the same
orientation as in a. The shallow binding cleft on top of the
globular molecule is formed by Tyr-34 and Trp-92. c, ribbon
representation of CBM6 in a perpendicular view with respect to
a, showing the second possible cleft (cleft B), which is
obstructed by a short loop in CBM6, situated on the concave face
of the -sheet
sandwich. a and c were produced with Molscript (45) and Raster3D
(46), whereas b was produced using GRASP (47).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2001,
276,
48580-48587)
copyright 2001.
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Secondary reference #1
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Title
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Homologous xylanases from clostridium thermocellum: evidence for bi-Functional activity, Synergism between xylanase catalytic modules and the presence of xylan-Binding domains in enzyme complexes.
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Authors
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A.C.Fernandes,
C.M.Fontes,
H.J.Gilbert,
G.P.Hazlewood,
T.H.Fernandes,
L.M.Ferreira.
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Ref.
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Biochem J, 1999,
342,
105-110.
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PubMed id
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