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PDBsum entry 1ok7
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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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Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases.
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Authors
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D.Y.Burnouf,
V.Olieric,
J.Wagner,
S.Fujii,
J.Reinbolt,
R.P.Fuchs,
P.Dumas.
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Ref.
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J Mol Biol, 2004,
335,
1187-1197.
[DOI no: ]
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PubMed id
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Abstract
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Most DNA polymerases interact with their cognate processive replication factor
through a small peptide, this interaction being absolutely required for their
function in vivo. We have solved the crystal structure of a complex between the
beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of
Pol IV (P16). The seven C-terminal residues bind to a pocket located at the
surface of one beta monomer. This region was previously identified as the
binding site of another beta clamp binding protein, the delta subunit of the
gamma complex. We show that peptide P16 competitively prevents
beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase
activities, suggesting that the site of interaction of the alpha subunit with
beta is identical with, or overlaps that of Pol IV. This common binding site for
delta, Pol IV and alpha subunit is shown to be formed by residues that are
highly conserved among many bacterial beta homologs, thus defining an
evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new
target for antibiotic drug design.
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Figure 1.
Figure 1. A, Ribbon representation of the b-ring with one
bound P16 peptide. Only the seven C-terminal residues of the
peptide were structured and modelled into the density map
(coloured in yellow). B, Fourier difference maps around the
visible part of P16 with (F[o] -F[c]) coefficients in red, and
with (2F[o] -F[c]) coefficients in blue.
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Figure 3.
Figure 3. A, Sequence alignment of the d subunit of g
complex and of DNA polymerase IV b-binding peptides with the
corresponding consensus sequence.[12.] The most conserved
residues are highlighted in blue and the red lines delimit
sub-sites 1 and 2 (see Results and Discussion). B, Schematic
representation of the b-binding pocket. Peptide P16 is drawn in
red, highly conserved b residues are boxed in green and less
conserved residues in open boxes. Green, black and open circles
identify b residues interacting with the most conserved residues
of peptide P16, i.e. residues L16, L14 and Q11, respectively.
Green and white bars on the right identify the conserved and
less conserved parts within the two sub-sites, respectively.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
335,
1187-1197)
copyright 2004.
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Secondary reference #1
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Title
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Three-Dimensional structure of the beta subunit of e. Coli DNA polymerase III holoenzyme: a sliding DNA clamp.
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Authors
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X.P.Kong,
R.Onrust,
M.O'Donnell,
J.Kuriyan.
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Ref.
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Cell, 1992,
69,
425-437.
[DOI no: ]
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PubMed id
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