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PDBsum entry 3ecc
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* Residue conservation analysis
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DOI no:
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Cell
135:623-634
(2008)
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PubMed id:
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Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators.
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M.L.Mott,
J.P.Erzberger,
M.M.Coons,
J.M.Berger.
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ABSTRACT
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The loading of oligomeric helicases onto replication origins marks an essential
step in replisome assembly. In cells, dedicated AAA+ ATPases regulate loading,
however, the mechanism by which these factors recruit and deposit helicases has
remained unclear. To better understand this process, we determined the structure
of the ATPase region of the bacterial helicase loader DnaC from Aquifex aeolicus
to 2.7 A resolution. The structure shows that DnaC is a close paralog of the
bacterial replication initiator, DnaA, and unexpectedly shares an ability to
form a helical assembly similar to that of ATP-bound DnaA. Complementation and
ssDNA-binding assays validate the importance of homomeric DnaC interactions,
while pull-down experiments show that the DnaC and DnaA AAA+ domains interact in
a nucleotide-dependent manner. These findings implicate DnaC as a molecular
adaptor that uses ATP-activated DnaA as a docking site for regulating the
recruitment and correct spatial deposition of the DnaB helicase onto origins.
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Selected figure(s)
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Figure 1.
Figure 1. Structure of DnaC[AAA+]
(A) Domain
representation of DnaC. The N-terminal helicase binding region
is colored gray and the central AAA+ domain is shown in red.
Numbers refer to amino acid positions. AAA+ motifs are
highlighted. WA, Walker-A; WB, Walker-B; SI, sensor-I; SII,
sensor-II; ISM, Initiator Specific Motif.
(B) Sequence
alignment of selected DnaC and DnaA homologs. Alignment was
generated by ClustalX (Thompson et al., 1997).
(C) Stereo
view of DnaC[AAA+]. Walker-A and -B motifs are blue and yellow,
respectively. The sensor-I residue is green and the Box VII
helix cyan. ADP and the coordinating magnesium ion (black) are
shown within the ATP binding cleft. An internal disordered
region is shown as a dotted line. This and all other molecular
figures were generated with PyMOL (pymol.sourceforge.net).
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Figure 6.
Figure 6. Model for DnaC/DnaA Crosstalk and Helicase
Deposition
(A) Structural model for oligomeric DnaC:DnaA
interactions. The figure was generated by superimposing the last
subunit of a six-subunit DnaC[AAA+] oligomer onto the end of a
twelve-subunit DnaA filament assembly. Axial and side views are
shown. Cyan spheres represent bound nucleotide.
(B) Model
for the symmetric loading of two replicative helicases at oriC.
Left: DnaA assembles at oriC and melts the DUE (purple strands).
Middle, (1): helicase loading on the bottom DUE strand is
facilitated through direct DnaA:DnaB interaction. Middle, (2):
DnaC, through a specific interaction with ATP-charged DnaA,
recruits the helicase destined for the top strand to oriC.
Right: ATP hydrolysis and loss of DnaC frees both DnaB hexamers
to migrate to their proper fork positions.
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The above figures are
reprinted
from an Open Access publication published by Cell Press:
Cell
(2008,
135,
623-634)
copyright 2008.
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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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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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H.Kawakami,
and
T.Katayama
(2010).
DnaA, ORC, and Cdc6: similarity beyond the domains of life and diversity.
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Biochem Cell Biol,
88,
49-62.
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L.Terradot,
and
A.Zawilak-Pawlik
(2010).
Structural insight into Helicobacter pylori DNA replication initiation.
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Gut Microbes,
1,
330-334.
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M.Botchan,
and
J.Berger
(2010).
DNA replication: making two forks from one prereplication complex.
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Mol Cell,
40,
860-861.
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M.K.Gupta,
J.Atkinson,
and
P.McGlynn
(2010).
DNA structure specificity conferred on a replicative helicase by its loader.
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J Biol Chem,
285,
979-987.
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M.Makowska-Grzyska,
and
J.M.Kaguni
(2010).
Primase directs the release of DnaC from DnaB.
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Mol Cell,
37,
90.
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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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W.H.Grainger,
C.Machón,
D.J.Scott,
and
P.Soultanas
(2010).
DnaB proteolysis in vivo regulates oligomerization and its localization at oriC in Bacillus subtilis.
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Nucleic Acids Res,
38,
2851-2864.
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W.K.Smits,
A.I.Goranov,
and
A.D.Grossman
(2010).
Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo.
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Mol Microbiol,
75,
452-461.
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W.Yang
(2010).
Lessons learned from UvrD helicase: mechanism for directional movement.
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Annu Rev Biophys,
39,
367-385.
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A.C.Leonard,
and
J.E.Grimwade
(2009).
Initiating chromosome replication in E. coli: it makes sense to recycle.
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Genes Dev,
23,
1145-1150.
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A.I.Goranov,
A.M.Breier,
H.Merrikh,
and
A.D.Grossman
(2009).
YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress.
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Mol Microbiol,
74,
454-466.
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D.Remus,
F.Beuron,
G.Tolun,
J.D.Griffith,
E.P.Morris,
and
J.F.Diffley
(2009).
Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing.
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Cell,
139,
719-730.
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G.Natrajan,
M.F.Noirot-Gros,
A.Zawilak-Pawlik,
U.Kapp,
and
L.Terradot
(2009).
The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria.
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Proc Natl Acad Sci U S A,
106,
21115-21120.
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PDB code:
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K.Kurokawa,
H.Mizumura,
T.Takaki,
Y.Ishii,
N.Ichihashi,
B.L.Lee,
and
K.Sekimizu
(2009).
Rapid exchange of bound ADP on the Staphylococcus aureus replication initiation protein DnaA.
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J Biol Chem,
284,
34201-34210.
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K.V.Loscha,
K.Jaudzems,
C.Ioannou,
X.C.Su,
F.R.Hill,
G.Otting,
N.E.Dixon,
and
E.Liepinsh
(2009).
A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader.
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Nucleic Acids Res,
37,
2395-2404.
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PDB code:
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M.L.Bochman,
and
A.Schwacha
(2009).
The Mcm complex: unwinding the mechanism of a replicative helicase.
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Microbiol Mol Biol Rev,
73,
652-683.
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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
