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PDBsum entry 2zle
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Contents |
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(+ 6 more)
396 a.a.
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346 a.a.
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References listed in PDB file
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Key reference
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Title
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Structural basis for the regulated protease and chaperone function of degp.
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Authors
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T.Krojer,
J.Sawa,
E.Schäfer,
H.R.Saibil,
M.Ehrmann,
T.Clausen.
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Ref.
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Nature, 2008,
453,
885-890.
[DOI no: ]
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PubMed id
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Abstract
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All organisms have to monitor the folding state of cellular proteins precisely.
The heat-shock protein DegP is a protein quality control factor in the bacterial
envelope that is involved in eliminating misfolded proteins and in the
biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms
underlying the regulated protease and chaperone function of DegP from
Escherichia coli. We show that binding of misfolded proteins transforms
hexameric DegP into large, catalytically active 12-meric and 24-meric multimers.
A structural analysis of these particles revealed that DegP represents a protein
packaging device whose central compartment is adaptable to the size and
concentration of substrate. Moreover, the inner cavity serves antagonistic
functions. Whereas the encapsulation of folded protomers of outer-membrane
proteins is protective and might allow safe transit through the periplasm,
misfolded proteins are eliminated in the molecular reaction chamber. Oligomer
reassembly and concomitant activation on substrate binding may also be critical
in regulating other HtrA proteases implicated in protein-folding diseases.
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Figure 2.
Figure 2: Regulation of protease activity by oligomer
reassembly. a, Ribbon plot of the protease domain of DegP[6]
(1kj9) and DegP[24], highlighting the mechanistically important
loops LA*, LD, L1, L2 and L3. Residues of the catalytic triad
(Asp 105, His 135 and Ala 210) are shown in stick mode and the
loop nomenclature used^12, ^41 is indicated. b, Electron density
of the active-site loops L1 and LD. The 2F[o] - F[c] simulated
annealing omit map was calculated at 3.0 Å resolution
(contoured at 1.1  )
after omitting loops L1 and LD from the refined model. The
oxyanion hole (blue sphere) and the main-chain carbonyl group of
Arg 207 are highlighted. The position of the latter oxygen is a
distinctive feature of proteolytically active HtrA proteases. c,
Denatured lysozyme and DegP[6] were incubated in different
ratios and the resulting complexes were analysed by SEC. Left:
incubation of different amounts of lysozyme (orange, 30  M;
red, 300 M;
blue, 600 M)
with DegP[6] (15 M).
Right: incubation of different amounts of DegP[6] (orange, 3
M;
red, 15 M;
blue, 65 M)
with lysozyme (170 M).
d, Brief incubation of wild-type DegP with casein (1 min,
magenta line) resulted in the formation of the DegP[24]–casein
complex (the pronounced low-molecular-mass peak represents
unprocessed casein). After completion of degradation (30 min,
green line), DegP recycled into its hexameric state. Composites
of individual elution peaks are indicated on the SDS gel; the
self-cleavage products of DegP are labelled DegP*.
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Figure 5.
Figure 5: Cryo-electron microscopy structure of the
DegP[12]–OMP complex. a, The asymmetric DegP[12]–OMP
complex viewed along the approximate three-fold (top) and
two-fold (bottom) axes. In the left panels the ribbon model of
the DegP dodecamer is overlaid with the semi-transparent
three-dimensional map. b, Central section of the DegP[12]–OMP
electron microscopy map with an OmpC monomer (blue) modelled in
the central density. The adjacent PDZ1 domains from neighbouring
trimers are coloured in cyan and magenta. Three catalytic triads
are coloured in red, green and blue and are shown magnified in
the lower panel. Scale bar, 100 Å.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
453,
885-890)
copyright 2008.
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