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PDBsum entry 1nqd
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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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A bacterial collagen-Binding domain with novel calcium-Binding motif controls domain orientation.
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Authors
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J.J.Wilson,
O.Matsushita,
A.Okabe,
J.Sakon.
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Ref.
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EMBO J, 2003,
22,
1743-1752.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a collagen-binding domain (CBD) with an N-terminal
domain linker from Clostridium histolyticum class I collagenase was determined
at 1.00 A resolution in the absence of calcium (1NQJ) and at 1.65 A resolution
in the presence of calcium (1NQD). The mature enzyme is composed of four
domains: a metalloprotease domain, a spacing domain and two CBDs. A
12-residue-long linker is found at the N-terminus of each CBD. In the absence of
calcium, the CBD reveals a beta-sheet sandwich fold with the linker adopting an
alpha-helix. The addition of calcium unwinds the linker and anchors it to the
distal side of the sandwich as a new beta-strand. The conformational change of
the linker upon calcium binding is confirmed by changes in the Stokes and
hydrodynamic radii as measured by size exclusion chromatography and by dynamic
light scattering with and without calcium. Furthermore, extensive mutagenesis of
conserved surface residues and collagen-binding studies allow us to identify the
collagen-binding surface of the protein and propose likely collagen-protein
binding models.
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Figure 2.
Figure 2 CBD in the presence and absence of calcium. (A) In the
high resolution apo-CBD structure, no calcium was observed, and
the N-terminus residues 895 -908 adopted an  -helix
conformation (colored red) in one molecule of the ASU. (B) In
the holo-CBD structure, two Ca^2+ ions were found (colored
orange), and the N-terminus residues 890 -908 continued the  -sheet
on the back face of the protein. Residues N963 -N966 were not
resolved. The tyrosine-rich surface is at the left and the back
face is at the right of each molecule.
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Figure 4.
Figure 4 Stereo diagram of the dual-calcium-binding site.
Holo-CBD is shown with coordinated Ca^2+ ions (orange spheres).
Calcium-binding residues are in 'ball-and-stick' rendering. The
orientation is similar to that of Figure 2. The calcium on the
right is coordinated to ligands with near square antiprismatic
geometry while the one on the left is coordinated to them with
near pentagonal bipyramidal geometry. This figure was prepared
using Molscript (Kraulis, 1991).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2003,
22,
1743-1752)
copyright 2003.
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