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PDBsum entry 1xec
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Structural protein
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PDB id
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1xec
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the dimeric protein core of decorin, The archetypal small leucine-Rich repeat proteoglycan.
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Authors
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P.G.Scott,
P.A.Mcewan,
C.M.Dodd,
E.M.Bergmann,
P.N.Bishop,
J.Bella.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
15633-15638.
[DOI no: ]
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PubMed id
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Abstract
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Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of
important biological functions that are mediated by its interactions with
extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is
the prototype of the family of small leucine-rich repeat proteoglycans and
proteins (SLRPs), characterized by a protein core composed of leucine-rich
repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal
structure of the dimeric protein core of decorin, the best characterized member
of the SLRP family. Each monomer adopts the curved solenoid fold characteristic
of LRR domains, with a parallel beta-sheet on the inside interwoven with loops
containing short segments of beta-strands, 3(10) helices, and polyproline II
helices on the outside. Two main features are unique to this structure. First,
decorin dimerizes through the concave surfaces of the LRR domains, which have
been implicated previously in protein-ligand interactions. The amount of surface
buried in this dimer rivals the buried surfaces of some of the highest-affinity
macromolecular complexes reported to date. Second, the C-terminal region adopts
an unusual capping motif that involves a laterally extended LRR and a disulfide
bond. This motif seems to be unique to SLRPs and has not been observed in any
other LRR protein structure to date. Possible implications of these features for
decorin ligand binding and SLRP function are discussed.
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Figure 3.
Fig. 3. Extent and sequence conservation of the dimer
interface. (a) View of the concave side of a decorin monomer.
Residues that are buried from solvent in the dimer are shown in
orange. (b) Two-dimensional representation of the surface
residues at the concave side of class I SLRPs. Yellow, residues
fully conserved in all three SLRPs; green, partially conserved
residues; black outline, the footprint of the decorin
dimerization interface. The relative positions and directions of
the 14  -strands that form the
concave side -sheet are indicated.
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Figure 4.
Fig. 4. Molecular interactions at the dimer interface. (a)
The aromatic ring of Phe-27 in one monomer (green) becomes
intercalated between the aromatic rings of two His residues in
the other monomer (red). This hydrophobic sandwich is part of an
extended hydrophobic array (see text). (b) Extensive
hydrogen-bonding networks (blue dotted lines) occur between the
two monomers.
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Secondary reference #1
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Title
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Light and X-Ray scattering show decorin to be a dimer in solution.
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Authors
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P.G.Scott,
J.G.Grossmann,
C.M.Dodd,
J.K.Sheehan,
P.N.Bishop.
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Ref.
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J Biol Chem, 2003,
278,
18353-18359.
[DOI no: ]
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PubMed id
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Figure 4.
Fig. 4. Effect of GdnHCl on elution behavior and
molecular weights of intact decorin and protein core. Smooth
curves show refractive index detector output and superimposed
plots show molecular weight versus volume. Panel A, Superose 12
column equilibrated in TBS (solid line) or in TBS containing 2.5
M GdnHCl (broken line). From left to right, intact natural
decorin in (1) TBS and (2) GdnHCl and protein core in (3) GdnHCl
and (4) TBS. Panel B, Superose 6 column equilibrated in TBS and
samples dissolved in TBS (solid line) or in TBS containing 2.5 M
GdnHCl (broken line).
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Figure 6.
Fig. 6. Representation of the shape of decorin core
protein based on the x-ray scattering profile shown in Fig. 5.
Two orthogonal orientations are shown on the left hand side. In
order to put the size and conformation of the restored shape
into perspective, a simple model based on the crystal structure
of YopM (34) is presented in the form of a ribbon showing two
monomers arranged as intertwined C shapes on the right hand
side. Scale bar represents 25 Å.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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