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PDBsum entry 1r91
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References listed in PDB file
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Key reference
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Title
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Clp protease complexes from photosynthetic and non-Photosynthetic plastids and mitochondria of plants, Their predicted three-Dimensional structures, And functional implications.
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Authors
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J.B.Peltier,
D.R.Ripoll,
G.Friso,
A.Rudella,
Y.Cai,
J.Ytterberg,
L.Giacomelli,
J.Pillardy,
K.J.Van wijk.
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Ref.
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J Biol Chem, 2004,
279,
4768-4781.
[DOI no: ]
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PubMed id
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Abstract
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Tetradecameric Clp protease core complexes in non-photosynthetic plastids of
roots, flower petals, and in chloroplasts of leaves of Arabidopsis thaliana were
purified based on native mass and isoelectric point and identified by mass
spectrometry. The stoichiometry between the subunits was determined. The
protease complex consisted of one to three copies of five different serine-type
protease Clp proteins (ClpP1,3-6) and four non-proteolytic ClpR proteins
(ClpR1-4). Three-dimensional homology modeling showed that the ClpP/R proteins
fit well together in a tetradecameric complex and also indicated unique
contributions for each protein. Lateral exit gates for proteolysis products are
proposed. In addition, ClpS1,2, unique to land plants, tightly interacted with
this core complex, with one copy of each per complex. The three-dimensional
modeling show that they do fit well on the axial sites of the ClpPR cores. In
contrast to plastids, plant mitochondria contained a single approximately
320-kDa homo-tetradecameric ClpP2 complex, without association of ClpR or ClpS
proteins. It is surprising that the Clp core composition appears identical in
all three plastid types, despite the remarkable differences in plastid proteome
composition. This suggests that regulation of plastid proteolysis by the Clp
machinery is not through differential regulation of ClpP/R/S gene expression,
but rather through substrate recognition mechanisms and regulated interaction of
chaperone-like molecules (ClpS1,2 and others) to the ClpP/R core.
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Figure 6.
FIG. 6. Structure alignment of the models for the ClpP/R
monomers with 1TYF [PDB]
, 1NZY [PDB]
, and 1HNO [PDB]
. The alignments are based on the structure alignment between
the 1TYF [PDB]
monomer and its structural neighbors.a, 1TYF [PDB]
eClpP;b, ConsRes indicates conserved residues in all the ClpP/R
sequences;c, Cat.Site indicates residues forming the catalytic
site;d, Put_Open indicates residues that are involved in the
putative opening in the Clp core;e, SS indicates the secondary
structure information of the specified molecule: E, extended; H,
helix; T, turn.
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Figure 9.
FIG. 9. Alignment of the ClpS sequences with the N-terminal
domain of eClpA. NT-eClpA denotes the N-terminal domain of eClpA
(PDB code 1K6K [PDB]
); COG542-eClpA indicates the consensus N-terminal domain of
eClpA structures found by BLAST (NCBI CD, COG0542.1,ClpA;
PSSM-Idm 10413); N domain denotes the Clp N-terminal domain
found in one or two copies at the N terminus of ClpA and ClpB
proteins from bacteria or eukaryotes. Color code: positions with
polar residue conservation in blue; charge conservation in red,
and hydrophobicity conservation in green. Conserved residues are
shown in boldface. The magenta (LL1) and orange (LL2) rectangles
indicate residues from two loop regions on ClpS1,2. The
equivalent loops in NT-eClpA possibly provide most of the
interacting surface when bound to eClpS.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
4768-4781)
copyright 2004.
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