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PDBsum entry 1jql
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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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Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of e. Coli DNA polymerase III.
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Authors
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D.Jeruzalmi,
O.Yurieva,
Y.Zhao,
M.Young,
J.Stewart,
M.Hingorani,
M.O'Donnell,
J.Kuriyan.
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Ref.
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Cell, 2001,
106,
417-428.
[DOI no: ]
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PubMed id
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Abstract
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The dimeric ring-shaped sliding clamp of E. coli DNA polymerase III (beta
subunit, homolog of eukaryotic PCNA) is loaded onto DNA by the clamp loader
gamma complex (homolog of eukaryotic Replication Factor C, RFC). The delta
subunit of the gamma complex binds to the beta ring and opens it. The crystal
structure of a beta:delta complex shows that delta, which is structurally
related to the delta' and gamma subunits of the gamma complex, is a molecular
wrench that induces or traps a conformational change in beta such that one of
its dimer interfaces is destabilized. Structural comparisons and molecular
dynamics simulations suggest a spring-loaded mechanism in which the beta ring
opens spontaneously once a dimer interface is perturbed by the delta wrench.
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Figure 2.
Figure 2. Structure of the β:δ Complex(A) View along the
edge of the β ring, centered on Domain 2 of β. (B) View
showing the intermolecular interface involving Domain 3 of β.
Structures shown in color are the β subunit and the δ subunit
from the crystal structure of the complex. For reference, a
second β monomer is shown in gray, taken from the crystal
structure of the dimeric form of β (Kong et al., 1992), PDB
code 2POL. The β-interaction element on δ (helix α4 and the
loop following it) is colored yellow, and the side chains of two
key hydrophobic residues of δ (Leu-73 and Phe-74) are shown
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Figure 5.
Figure 5. Similarity in the Binding Modes of p21 and RB69
DNA Polymerase to the Interaction of δ with βThe structure of
the β subunit in the β:δ complex is shown in gray and cyan.
The structures of PCNA complexed to p21 (Gulbis et al., 1996)
(PDB code 1AXC) and gp45 of RB69 complexed to a segment of RB69
DNA polymerase (Shamoo and Steitz, 1999) (PDB code 1B8H) were
superimposed individually onto the structure of the β subunit
by using the β strands at this interdomain interface to overlay
the structures. The structure of the p21 peptide (orange) and
the RB69 DNA polymerase tethering segment (yellow) are shown,
but were not used in the structural superposition. The structure
of δ is shown in green. PCNA and gp45 are not shown
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
106,
417-428)
copyright 2001.
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