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PDBsum entry 1tyf
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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 structure of clpp at 2.3 a resolution suggests a model for ATP-Dependent proteolysis.
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Authors
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J.Wang,
J.A.Hartling,
J.M.Flanagan.
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Ref.
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Cell, 1997,
91,
447-456.
[DOI no: ]
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PubMed id
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Abstract
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We have determined the crystal structure of the proteolytic component of the
caseinolytic Clp protease (ClpP) from E. coli at 2.3 A resolution using an ab
initio phasing procedure that exploits the internal 14-fold symmetry of the
oligomer. The structure of a ClpP monomer has a distinct fold that defines a
fifth structural family of serine proteases but a conserved catalytic apparatus.
The active protease resembles a hollow, solid-walled cylinder composed of two
7-fold symmetric rings stacked back-to-back. Its 14 proteolytic active sites are
located within a central, roughly spherical chamber approximately 51 A in
diameter. Access to the proteolytic chamber is controlled by two axial pores,
each having a minimum diameter of approximately 10 A. From the structural
features of ClpP, we suggest a model for its action in degrading proteins.
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Figure 1.
Figure 1. Electron Density Map of the Region between Helix
C and Strand 5The |F[o]|exp(iφ^ave) electron density map is
contoured at 1.5 σ and superimposed upon the refined model.
|Fo| and φ^ave are the observed amplitudes, and the calculated
phases after NCS averaging with RAVE ([23]), respectively. In
this map, the turn between helix C and strand 5 (residues
80–85) is stabilized by a solvent molecule or a cation. The
refined model is superimposed on the density as a wire model. A
water molecule and the unidentified solvent/cation molecule are
shown as magenta spheres.
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Figure 5.
Figure 5. Subunit Interface in ClpP(A) The intra-ring
association of ClpP monomers is shown as a ribbon diagram.
Monomer 1 is shown in gray, monomer 2 in olive; residues in the
catalytic triad and those that stabilize the oxyanion
intermediate are represented as spheres: Ser-97 is magenta,
His-122 is green, Asp-171 is red, and Gly-68 and Met-98 are
olive. Dimerization of the two rings of heptamers results in the
formation of an antiparallel β sheet comprising strand 9 from
two NCS-related subunits. The small (+) represents the two-fold
axis relating the stacked monomers in opposing rings.(B) The
intraring contacts between monomers are shown; in one ring,
monomer 1 (gray) in (A) packs against monomer 3 shown in blue,
and in the opposing ring, monomer 2 (olive) in (A) packs against
monomer 4 shown in cyan. As in (A), the catalytic residues are
shown as spheres. As in (A), the small (+) represents the
location of the two-fold axis relating stacked monomers; the
large (+) represents the location of a second two-fold axis
that lies between each pair of interring subunits.(C) A CPK
representation of (B) showing the interdigitation of the
monomers.(D) A solvent-accessible surface representation of (B)
shows the connection between adjacent active site clefts in the
heptameric ring. The active sites in opposing heptamers are also
connected by channels that lie along the two-fold axes of the
oligomer, giving the surface of the proteolytic chamber a
zigzag-like appearance.(E) A schematic representation of two
putative models of substrate binding. Strands 9 are drawn as
unshaded arrows and heptapeptides as shaded arrows. Dashed lines
represent possible connections between hepta-peptides in a
continuous substrate. Residues in the catalytic triads are drawn
as spheres.(F) A longitudinal section of a space-filling model
colored according to hydrophobicity. The apical and outer
equatorial surfaces are enriched in charged residues, whereas
the inner surface of the chamber is largely hydrophobic. In
this representation, hydrophobic residues (Tyr, Phe, Leu, Ile,
Met, Val, Pro, and Ala) are colored in yellow, while charged
residues are colored in blue (Lys and Arg) and red (Asp and
Glu), respectively. All other residues are colored in gray.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1997,
91,
447-456)
copyright 1997.
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Secondary reference #1
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Title
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Sequence and structure of clp p, The proteolytic component of the ATP-Dependent clp protease of escherichia coli.
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Authors
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M.R.Maurizi,
W.P.Clark,
Y.Katayama,
S.Rudikoff,
J.Pumphrey,
B.Bowers,
S.Gottesman.
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Ref.
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J Biol Chem, 1990,
265,
12536-12545.
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PubMed id
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