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PDBsum entry 1r6b
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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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Crystallographic investigation of peptide binding sites in the n-Domain of the clpa chaperone.
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Authors
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D.Xia,
L.Esser,
S.K.Singh,
F.Guo,
M.R.Maurizi.
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Ref.
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J Struct Biol, 2004,
146,
166-179.
[DOI no: ]
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PubMed id
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Abstract
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Escherichia coli ClpA, an Hsp100/Clp chaperone and an integral component of the
ATP-dependent ClpAP protease, participates in the dissolution and degradation of
regulatory proteins and protein aggregates. ClpA consists of three functional
domains: an N-terminal domain and two ATPase domains, D1 and D2. The N-domain is
attached to D1 by a mobile linker and is made up of two tightly bound,
identically folded alpha-helical bundles related by a pseudo 2-fold symmetry.
Between the halves of the pseudo-dimer is a large flexible acidic loop that
becomes better ordered upon binding of the small adaptor protein, ClpS. We have
identified a number of structural features in the N-domain, including a Zn(++)
binding motif, several interfaces for binding to ClpS, and a prominent
hydrophobic surface area that binds peptides in different configurations. These
structural motifs may contribute to binding of protein or peptide substrates
with weak affinity and broad specificity. Kinetic studies comparing wild-type
ClpA to a mutant ClpA with its N-domain deleted show that the N-domains
contribute to the binding of a non-specific protein substrate but not of a
folded substrate with the specific SsrA recognition tag. A functional model is
proposed in which the N-domains in ClpA function as tentacles to weakly hold on
to proteins thereby enhancing local substrate concentration.
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Secondary reference #1
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Title
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Crystal structure of clpa, An hsp100 chaperone and regulator of clpap protease.
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Authors
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F.Guo,
M.R.Maurizi,
L.Esser,
D.Xia.
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Ref.
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J Biol Chem, 2002,
277,
46743-46752.
[DOI no: ]
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PubMed id
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Figure 5.
Fig. 5. Hexameric model of ClpA. Electrostatic potential
surface of the modeled planar ClpA hexagon as rendered in GRASP,
with negative potential in red, positive in blue, and neutral in
white. a, the hexagonal ring is viewed along the 6-fold axis
with the D1 domains facing out. The hexagon has a crenated edge
and maximum diameter of 170 Å. The larger crenations are
made by the six N-domains, which are attached to the outer edge
of the D1 domains; the smaller crenations are formed by
extensions of the D2-small domains. b, the D2 side is facing
out, showing the wide opening of the central cavity (red) and
residues forming part of the ClpP loop (yellow). c, side view of
the modeled ClpA hexagonal ring. The height is about 87 Å.
The six subunits are shown in different colors. D1 and D2 from
the same ClpA subunit are tilted with respect to the ring axis
and make little contact with each other. Each domain makes
extensive contacts with both D1 and D2 of a neighboring subunit.
d, cross section through the center and parallel to the 6-fold
axis of the modeled ClpA hexagonal ring. The surface of the
central cavity is colored to show the three negatively charged
belts (red) and the hydrophobic surfaces surrounding the
channels (gray). The borders of the cavity are outlined in
black. The two constrictions and the two compartments are as
labeled. The positions for the three remaining ClpP loop are
indicated in yellow.
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Figure 6.
Fig. 6. A hypothetical model describing transitions of
ClpA subunits in solution to form a spiral in crystal in the
presence of ADP and to assemble into a planar hexamer in
solution in the presence of ATP. ClpA subunits are postulated to
undergo an open and a closed conformation by rotating D2 with
respect to D1 via the hinge between two domains.
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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