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Contents |
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366 a.a.
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338 a.a.
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334 a.a.
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* Residue conservation analysis
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PDB id:
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Transferase
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Title:
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Crystal structure of the processivity clamp loader gamma complex of e. Coli DNA polymerase iii
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Structure:
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DNA polymerase iii subunit gamma. Chain: a, b, c. Engineered: yes. DNA polymerase iii, delta subunit. Chain: d. Engineered: yes. DNA polymerase iii, delta' subunit. Chain: e. Engineered: yes
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Source:
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Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
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Biol. unit:
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Pentamer (from
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Resolution:
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2.70Å
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R-factor:
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0.268
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R-free:
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0.304
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Authors:
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D.Jeruzalmi,M.O'Donnell,J.Kuriyan
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Key ref:
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D.Jeruzalmi
et al.
(2001).
Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III.
Cell,
106,
429-441.
PubMed id:
DOI:
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Date:
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10-Aug-01
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Release date:
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26-Sep-01
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PROCHECK
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Headers
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References
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P06710
(DPO3X_ECOLI) -
DNA polymerase III subunit tau from Escherichia coli (strain K12)
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Seq:
Struc:
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643 a.a.
366 a.a.
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Enzyme class:
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Chains A, B, C, D, E:
E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Cell
106:429-441
(2001)
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PubMed id:
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Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III.
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D.Jeruzalmi,
M.O'Donnell,
J.Kuriyan.
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ABSTRACT
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The gamma complex, an AAA+ ATPase, is the bacterial homolog of eukaryotic
replication factor C (RFC) that loads the sliding clamp (beta, homologous to
PCNA) onto DNA. The 2.7/3.0 A crystal structure of gamma complex reveals a
pentameric arrangement of subunits, with stoichiometry delta':gamma(3):delta.
The C-terminal domains of the subunits form a circular collar that supports an
asymmetric arrangement of the N-terminal ATP binding domains of the gamma motor
and the structurally related domains of the delta' stator and the delta wrench.
The structure suggests a mechanism by which the gamma complex switches between a
closed state, in which the beta-interacting element of delta is hidden by
delta', and an open form similar to the crystal structure, in which delta is
free to bind to beta.
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Selected figure(s)
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Figure 3.
Figure 3. γ:γ Interfacial Nucleotide Binding Sites
Compared to the NSF Homolog p97(A) The nucleotide binding site
of p97 (left) (Zhang et al., 2000) (PDB code 1E32) is compared
to that of γ2 (at the γ1-γ2 interface, middle) and of γ3 (at
the γ2-γ3 interface, right). For the γ structures, Domains I
and II are colored, and Domain III is shown in gray. A schematic
representation of the Domain I–II units is shown below the
structures. ADP bound to p97 is shown at the active site of γ2
(middle) and γ3 (right) for reference. The arginine side chains
of the Sensor 1 region are shown in dark blue at each
interface.(B) The Sensor 1 region of γ1 is buried at the
γ1-γ2 interface. On the left, the γ1-γ2 pair of subunits is
shown, with the molecular surface of γ2 colored in gray,
highlighted in red where γ1 contacts the γ2 surface. γ1 is
shown as a green tube representing the backbone, with the Sensor
1 region colored magenta. γ2 is shown with the surface removed
on the right
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Figure 4.
Figure 4. The δ′ Stator Is Unlikely to Cause Closure of
the Adjacent γ1 ATP Binding SiteOn the left, the γ1 (green)
and γ2 (red) pair of subunits is shown, with Sensor 1 of γ1
(magenta) positioned near the ATP binding site of γ2 (indicated
in gray). The first helix of Domain III of γ1, α10, is shown
as a magenta tube to highlight the flexible linker connecting it
to the last helix of Domain II. On the right, γ2 is shown
again, in the same orientation as on the left (red). The γ1
subunit is replaced by δ′ (orange), which has been
superimposed on γ1 using the C-terminal domain. Note that helix
α10 in δ′ is extended at its N terminus relative to the
structure seen in γ1, so that the connection to Domain II no
longer appears to be flexible. The overall conformation of δ′
is more closed than that of γ1, so that the Sensor 1 region of
δ′ is no longer located as close to the ATP binding site of
γ2 as that of γ1
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
106,
429-441)
copyright 2001.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.E.Glynn,
A.R.Nager,
T.A.Baker,
and
R.T.Sauer
(2012).
Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine.
|
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Nat Struct Mol Biol,
19,
616-622.
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A.Y.Park,
and
C.V.Robinson
(2011).
Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination.
|
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Crit Rev Biochem Mol Biol,
46,
152-164.
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|
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|
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C.S.McHenry
(2011).
Breaking the rules: bacteria that use several DNA polymerase IIIs.
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EMBO Rep,
12,
408-414.
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|
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K.E.Duderstadt,
K.Chuang,
and
J.M.Berger
(2011).
DNA stretching by bacterial initiators promotes replication origin opening.
|
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Nature,
478,
209-213.
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PDB code:
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L.Johnsen,
I.Flåtten,
Morigen,
B.Dalhus,
M.Bjørås,
T.Waldminghaus,
and
K.Skarstad
(2011).
The G157C mutation in the Escherichia coli sliding clamp specifically affects initiation of replication.
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Mol Microbiol,
79,
433-446.
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PDB code:
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N.A.Tanner,
G.Tolun,
J.J.Loparo,
S.Jergic,
J.D.Griffith,
N.E.Dixon,
and
A.M.van Oijen
(2011).
E. coli DNA replication in the absence of free β clamps.
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EMBO J,
30,
1830-1840.
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|
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A.Politis,
A.Y.Park,
S.J.Hyung,
D.Barsky,
B.T.Ruotolo,
and
C.V.Robinson
(2010).
Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes.
|
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PLoS One,
5,
e12080.
|
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|
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A.Y.Park,
S.Jergic,
A.Politis,
B.T.Ruotolo,
D.Hirshberg,
L.L.Jessop,
J.L.Beck,
D.Barsky,
M.O'Donnell,
N.E.Dixon,
and
C.V.Robinson
(2010).
A single subunit directs the assembly of the Escherichia coli DNA sliding clamp loader.
|
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Structure,
18,
285-292.
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|
|
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|
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B.P.Pedersen,
J.P.Morth,
and
P.Nissen
(2010).
Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history.
|
| |
Acta Crystallogr D Biol Crystallogr,
66,
309-313.
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C.D.Downey,
and
C.S.McHenry
(2010).
Chaperoning of a replicative polymerase onto a newly assembled DNA-bound sliding clamp by the clamp loader.
|
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Mol Cell,
37,
481-491.
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|
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C.Zhao,
E.A.Matveeva,
Q.Ren,
and
S.W.Whiteheart
(2010).
Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains.
|
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J Biol Chem,
285,
761-772.
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|
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H.G.Dallmann,
O.J.Fackelmayer,
G.Tomer,
J.Chen,
A.Wiktor-Becker,
T.Ferrara,
C.Pope,
M.T.Oliveira,
P.M.Burgers,
L.S.Kaguni,
and
C.S.McHenry
(2010).
Parallel multiplicative target screening against divergent bacterial replicases: identification of specific inhibitors with broad spectrum potential.
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Biochemistry,
49,
2551-2562.
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M.D.Sutton
(2010).
Coordinating DNA polymerase traffic during high and low fidelity synthesis.
|
| |
Biochim Biophys Acta,
1804,
1167-1179.
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|
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|
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N.M.Dupes,
B.W.Walsh,
A.D.Klocko,
J.S.Lenhart,
H.L.Peterson,
D.A.Gessert,
C.E.Pavlick,
and
L.A.Simmons
(2010).
Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair.
|
| |
J Bacteriol,
192,
3452-3463.
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|
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O.Parnas,
A.Zipin-Roitman,
B.Pfander,
B.Liefshitz,
Y.Mazor,
S.Ben-Aroya,
S.Jentsch,
and
M.Kupiec
(2010).
Elg1, an alternative subunit of the RFC clamp loader, preferentially interacts with SUMOylated PCNA.
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EMBO J,
29,
2611-2622.
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R.McNally,
G.D.Bowman,
E.R.Goedken,
M.O'Donnell,
and
J.Kuriyan
(2010).
Analysis of the role of PCNA-DNA contacts during clamp loading.
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BMC Struct Biol,
10,
3.
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PDB code:
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T.C.Mueser,
J.M.Hinerman,
J.M.Devos,
R.A.Boyer,
and
K.J.Williams
(2010).
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
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Virol J,
7,
359.
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|
|
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|
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Z.Zhuang,
and
Y.Ai
(2010).
Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis.
|
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Biochim Biophys Acta,
1804,
1081-1093.
|
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|
|
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|
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A.R.Parks,
Z.Li,
Q.Shi,
R.M.Owens,
M.M.Jin,
and
J.E.Peters
(2009).
Transposition into replicating DNA occurs through interaction with the processivity factor.
|
| |
Cell,
138,
685-695.
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|
|
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|
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F.J.López de Saro
(2009).
Regulation of interactions with sliding clamps during DNA replication and repair.
|
| |
Curr Genomics,
10,
206-215.
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|
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J.A.Thompson,
C.O.Paschall,
M.O'Donnell,
and
L.B.Bloom
(2009).
A slow ATP-induced conformational change limits the rate of DNA binding but not the rate of beta clamp binding by the escherichia coli gamma complex clamp loader.
|
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J Biol Chem,
284,
32147-32157.
|
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|
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K.R.Simonetta,
S.L.Kazmirski,
E.R.Goedken,
A.J.Cantor,
B.A.Kelch,
R.McNally,
S.N.Seyedin,
D.L.Makino,
M.O'Donnell,
and
J.Kuriyan
(2009).
The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
|
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Cell,
137,
659-671.
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PDB codes:
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L.B.Bloom
(2009).
Loading clamps for DNA replication and repair.
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DNA Repair (Amst),
8,
570-578.
|
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|
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|
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M.L.Bochman,
and
A.Schwacha
(2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
|
| |
Microbiol Mol Biol Rev,
73,
652-683.
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|
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M.S.Park,
and
M.O'Donnell
(2009).
The clamp loader assembles the beta clamp onto either a 3' or 5' primer terminus: the underlying basis favoring 3' loading.
|
| |
J Biol Chem,
284,
31473-31483.
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M.Suga,
S.Maeda,
S.Nakagawa,
E.Yamashita,
and
T.Tsukihara
(2009).
A description of the structural determination procedures of a gap junction channel at 3.5 A resolution.
|
| |
Acta Crystallogr D Biol Crystallogr,
65,
758-766.
|
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Q.Yuan,
and
C.S.McHenry
(2009).
Strand displacement by DNA polymerase III occurs through a tau-psi-chi link to single-stranded DNA-binding protein coating the lagging strand template.
|
| |
J Biol Chem,
284,
31672-31679.
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|
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S.G.Anderson,
J.A.Thompson,
C.O.Paschall,
M.O'Donnell,
and
L.B.Bloom
(2009).
Temporal correlation of DNA binding, ATP hydrolysis, and clamp release in the clamp loading reaction catalyzed by the Escherichia coli gamma complex.
|
| |
Biochemistry,
48,
8516-8527.
|
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|
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S.K.Scouten Ponticelli,
J.M.Duzen,
and
M.D.Sutton
(2009).
Contributions of the individual hydrophobic clefts of the Escherichia coli beta sliding clamp to clamp loading, DNA replication and clamp recycling.
|
| |
Nucleic Acids Res,
37,
2796-2809.
|
|
|
|
|
|
|
Y.H.Chen,
Y.Lin,
A.Yoshinaga,
B.Chhotani,
J.L.Lorenzini,
A.A.Crofts,
S.Mei,
R.I.Mackie,
Y.Ishino,
and
I.K.Cann
(2009).
Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans.
|
| |
J Bacteriol,
191,
6539-6549.
|
|
|
|
|
|
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E.J.Enemark,
and
L.Joshua-Tor
(2008).
On helicases and other motor proteins.
|
| |
Curr Opin Struct Biol,
18,
243-257.
|
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M.L.Bochman,
S.P.Bell,
and
A.Schwacha
(2008).
Subunit organization of Mcm2-7 and the unequal role of active sites in ATP hydrolysis and viability.
|
| |
Mol Cell Biol,
28,
5865-5873.
|
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|
|
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|
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M.L.Mott,
J.P.Erzberger,
M.M.Coons,
and
J.M.Berger
(2008).
Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators.
|
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Cell,
135,
623-634.
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PDB codes:
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M.Su'etsugu,
K.Nakamura,
K.Keyamura,
Y.Kudo,
and
T.Katayama
(2008).
Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis.
|
| |
J Biol Chem,
283,
36118-36131.
|
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|
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|
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N.A.Tanner,
S.M.Hamdan,
S.Jergic,
P.M.Schaeffer,
N.E.Dixon,
and
A.M.van Oijen
(2008).
Single-molecule studies of fork dynamics in Escherichia coli DNA replication.
|
| |
Nat Struct Mol Biol,
15,
170-176.
|
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|
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|
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N.Y.Yao,
and
M.O'Donnell
(2008).
Replisome dynamics and use of DNA trombone loops to bypass replication blocks.
|
| |
Mol Biosyst,
4,
1075-1084.
|
|
|
|
|
|
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P.Pietroni,
and
P.H.von Hippel
(2008).
Multiple ATP binding is required to stabilize the "activated" (clamp open) clamp loader of the t4 DNA replication complex.
|
| |
J Biol Chem,
283,
28338-28353.
|
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|
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|
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R.D.Shereda,
A.G.Kozlov,
T.M.Lohman,
M.M.Cox,
and
J.L.Keck
(2008).
SSB as an organizer/mobilizer of genome maintenance complexes.
|
| |
Crit Rev Biochem Mol Biol,
43,
289-318.
|
|
|
|
|
|
|
S.Chen,
M.M.Coman,
M.Sakato,
M.O'Donnell,
and
M.M.Hingorani
(2008).
Conserved residues in the delta subunit help the E. coli clamp loader, gamma complex, target primer-template DNA for clamp assembly.
|
| |
Nucleic Acids Res,
36,
3274-3286.
|
|
|
|
|
|
|
A.F.Neuwald
(2007).
The CHAIN program: forging evolutionary links to underlying mechanisms.
|
| |
Trends Biochem Sci,
32,
487-493.
|
|
|
|
|
|
|
L.Knizewski,
L.N.Kinch,
N.V.Grishin,
L.Rychlewski,
and
K.Ginalski
(2007).
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
|
| |
BMC Struct Biol,
7,
40.
|
|
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|
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|
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P.McInerney,
A.Johnson,
F.Katz,
and
M.O'Donnell
(2007).
Characterization of a triple DNA polymerase replisome.
|
| |
Mol Cell,
27,
527-538.
|
|
|
|
|
|
|
S.G.Anderson,
C.R.Williams,
M.O'donnell,
and
L.B.Bloom
(2007).
A function for the psi subunit in loading the Escherichia coli DNA polymerase sliding clamp.
|
| |
J Biol Chem,
282,
7035-7045.
|
|
|
|
|
|
|
S.Jergic,
K.Ozawa,
N.K.Williams,
X.C.Su,
D.D.Scott,
S.M.Hamdan,
J.A.Crowther,
G.Otting,
and
N.E.Dixon
(2007).
The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit.
|
| |
Nucleic Acids Res,
35,
2813-2824.
|
|
|
|
|
|
|
W.Zhu,
C.Ukomadu,
S.Jha,
T.Senga,
S.K.Dhar,
J.A.Wohlschlegel,
L.K.Nutt,
S.Kornbluth,
and
A.Dutta
(2007).
Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication.
|
| |
Genes Dev,
21,
2288-2299.
|
|
|
|
|
|
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X.C.Su,
S.Jergic,
M.A.Keniry,
N.E.Dixon,
and
G.Otting
(2007).
Solution structure of Domains IVa and V of the tau subunit of Escherichia coli DNA polymerase III and interaction with the alpha subunit.
|
| |
Nucleic Acids Res,
35,
2825-2832.
|
|
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PDB code:
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A.F.Neuwald
(2006).
Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.
|
| |
Nucleic Acids Res,
34,
5280-5290.
|
|
|
|
|
|
|
A.Johnson,
N.Y.Yao,
G.D.Bowman,
J.Kuriyan,
and
M.O'Donnell
(2006).
The replication factor C clamp loader requires arginine finger sensors to drive DNA binding and proliferating cell nuclear antigen loading.
|
| |
J Biol Chem,
281,
35531-35543.
|
|
|
|
|
|
|
A.Seybert,
M.R.Singleton,
N.Cook,
D.R.Hall,
and
D.B.Wigley
(2006).
Communication between subunits within an archaeal clamp-loader complex.
|
| |
EMBO J,
25,
2209-2218.
|
|
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PDB codes:
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A.W.Serohijos,
Y.Chen,
F.Ding,
T.C.Elston,
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Clamp and clamp loader structures of the human checkpoint protein complexes, Rad9-1-1 and Rad17-RFC.
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Genes Cells,
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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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Cell,
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PDB codes:
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L.B.Bloom,
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(2001).
A sliding clamp monkey wrench.
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Nat Struct Biol,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
