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PDBsum entry 2reb
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DNA binding protein
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PDB id
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2reb
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Contents |
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* Residue conservation analysis
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Nature
355:318-325
(1992)
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PubMed id:
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The structure of the E. coli recA protein monomer and polymer.
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R.M.Story,
I.T.Weber,
T.A.Steitz.
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ABSTRACT
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The crystal structure of the recA protein from Escherichia coli at 2.3-A
resolution reveals a major domain that binds ADP and probably single- and
double-stranded DNA. Two smaller subdomains at the N and C termini protrude from
the protein and respectively stabilize a 6(1) helical polymer of protein
subunits and interpolymer bundles. This polymer structure closely resembles that
of recA/DNA filaments determined by electron microscopy. Mutations in recA
protein that enhance coprotease, DNA-binding and/or strand-exchange activity can
be explained if the interpolymer interactions in the crystal reflect a
regulatory mechanism in vivo.
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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.Glatt,
J.Létoquart,
C.Faux,
N.M.Taylor,
B.Séraphin,
and
C.W.Müller
(2012).
The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase.
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Nat Struct Mol Biol,
19,
314-320.
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PDB code:
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A.Y.Lyubimov,
M.Strycharska,
and
J.M.Berger
(2011).
The nuts and bolts of ring-translocase structure and mechanism.
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Curr Opin Struct Biol,
21,
240-248.
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C.Bustamante,
W.Cheng,
Y.X.Mejia,
and
Y.X.Meija
(2011).
Revisiting the central dogma one molecule at a time.
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Cell,
144,
480-497.
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J.Strohmeier,
I.Hertel,
U.Diederichsen,
M.G.Rudolph,
and
D.Klostermeier
(2011).
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
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Biol Chem,
392,
357-369.
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PDB codes:
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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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A.L.Okorokov,
Y.L.Chaban,
D.V.Bugreev,
J.Hodgkinson,
A.V.Mazin,
and
E.V.Orlova
(2010).
Structure of the hDmc1-ssDNA filament reveals the principles of its architecture.
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PLoS One,
5,
e8586.
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I.V.Bakhlanova,
A.V.Dudkina,
D.M.Baitin,
K.L.Knight,
M.M.Cox,
and
V.A.Lanzov
(2010).
Modulating cellular recombination potential through alterations in RecA structure and regulation.
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Mol Microbiol,
78,
1523-1538.
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L.T.Chen,
and
A.H.Wang
(2010).
A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo.
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Nucleic Acids Res,
38,
4361-4371.
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R.A.Forties,
and
R.Bundschuh
(2010).
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
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Bioinformatics,
26,
61-67.
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R.K.Chittela,
and
J.K.Sainis
(2010).
Plant DNA recombinases: a long way to go.
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J Nucleic Acids,
2010,
0.
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R.L.Britt,
N.Haruta,
S.L.Lusetti,
S.Chitteni-Pattu,
R.B.Inman,
and
M.M.Cox
(2010).
Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange.
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J Biol Chem,
285,
3211-3226.
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R.Morita,
S.Nakane,
A.Shimada,
M.Inoue,
H.Iino,
T.Wakamatsu,
K.Fukui,
N.Nakagawa,
R.Masui,
and
S.Kuramitsu
(2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
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J Nucleic Acids,
2010,
179594.
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S.Colavito,
R.Prakash,
and
P.Sung
(2010).
Promotion and regulation of homologous recombination by DNA helicases.
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Methods,
51,
329-335.
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A.A.Grigorescu,
J.H.Vissers,
D.Ristic,
Y.Z.Pigli,
T.W.Lynch,
C.Wyman,
and
P.A.Rice
(2009).
Inter-subunit interactions that coordinate Rad51's activities.
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Nucleic Acids Res,
37,
557-567.
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A.Reymer,
K.Frykholm,
K.Morimatsu,
M.Takahashi,
and
B.Nordén
(2009).
Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy.
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Proc Natl Acad Sci U S A,
106,
13248-13253.
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C.A.Belon,
and
D.N.Frick
(2009).
Helicase inhibitors as specifically targeted antiviral therapy for hepatitis C.
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Future Virol,
4,
277-293.
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C.D.Lee,
and
T.F.Wang
(2009).
The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination.
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J Biomed Sci,
16,
37.
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D.Klostermeier,
and
M.G.Rudolph
(2009).
A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility.
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Nucleic Acids Res,
37,
421-430.
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PDB codes:
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D.Lucarelli,
Y.A.Wang,
V.E.Galkin,
X.Yu,
D.B.Wigley,
and
E.H.Egelman
(2009).
The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.
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J Mol Biol,
391,
269-274.
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J.A.Steen,
T.L.Bannam,
W.L.Teng,
R.J.Devenish,
and
J.I.Rood
(2009).
The putative coupling protein TcpA interacts with other pCW3-encoded proteins to form an essential part of the conjugation complex.
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J Bacteriol,
191,
2926-2933.
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J.E.Long,
N.Renzette,
and
S.J.Sandler
(2009).
Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12.
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Mol Microbiol,
73,
226-239.
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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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M.M.Cox
(2009).
A new look at the human Rad51 protein.
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Proc Natl Acad Sci U S A,
106,
13147-13148.
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N.D.Thomsen,
and
J.M.Berger
(2009).
Running in reverse: the structural basis for translocation polarity in hexameric helicases.
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Cell,
139,
523-534.
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PDB code:
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N.Handa,
I.Amitani,
N.Gumlaw,
S.J.Sandler,
and
S.C.Kowalczykowski
(2009).
Single Molecule Analysis of a Red Fluorescent RecA Protein Reveals a Defect in Nucleoprotein Filament Nucleation That Relates to Its Reduced Biological Functions.
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J Biol Chem,
284,
18664-18673.
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R.B.Robertson,
D.N.Moses,
Y.Kwon,
P.Chan,
W.Zhao,
P.Chi,
H.Klein,
P.Sung,
and
E.C.Greene
(2009).
Visualizing the disassembly of S. cerevisiae Rad51 nucleoprotein filaments.
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J Mol Biol,
388,
703-720.
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X.P.Zhang,
V.E.Galkin,
X.Yu,
E.H.Egelman,
and
W.D.Heyer
(2009).
Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity.
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Nucleic Acids Res,
37,
158-171.
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Y.H.Lo,
K.L.Tsai,
Y.J.Sun,
W.T.Chen,
C.Y.Huang,
and
C.D.Hsiao
(2009).
The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
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Nucleic Acids Res,
37,
804-814.
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PDB codes:
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Y.Li,
Y.He,
and
Y.Luo
(2009).
Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.
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Acta Crystallogr D Biol Crystallogr,
65,
602-610.
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PDB codes:
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A.I.Roca,
A.E.Almada,
and
A.C.Abajian
(2008).
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
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BMC Bioinformatics,
9,
554.
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J.M.Cox,
H.Li,
E.A.Wood,
S.Chitteni-Pattu,
R.B.Inman,
and
M.M.Cox
(2008).
Defective Dissociation of a "Slow" RecA Mutant Protein Imparts an Escherichia coli Growth Defect.
|
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J Biol Chem,
283,
24909-24921.
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J.R.Prabu,
G.P.Manjunath,
N.R.Chandra,
K.Muniyappa,
and
M.Vijayan
(2008).
Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes.
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Acta Crystallogr D Biol Crystallogr,
64,
1146-1157.
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PDB codes:
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N.D.Thomsen,
and
J.M.Berger
(2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
|
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Mol Microbiol,
69,
1071-1090.
|
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S.C.Kowalczykowski
(2008).
Structural biology: snapshots of DNA repair.
|
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Nature,
453,
463-466.
|
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S.H.Leuba,
S.P.Anand,
J.M.Harp,
and
S.A.Khan
(2008).
Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time.
|
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Chromosome Res,
16,
451-467.
|
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T.Saito,
and
M.Gale
(2008).
Differential recognition of double-stranded RNA by RIG-I-like receptors in antiviral immunity.
|
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J Exp Med,
205,
1523-1527.
|
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V.E.Galkin,
X.Yu,
J.Bielnicki,
J.Heuser,
C.P.Ewing,
P.Guerry,
and
E.H.Egelman
(2008).
Divergence of quaternary structures among bacterial flagellar filaments.
|
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Science,
320,
382-385.
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Z.Chen,
H.Yang,
and
N.P.Pavletich
(2008).
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
|
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Nature,
453,
489-484.
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PDB codes:
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D.J.Cline,
S.L.Holt,
and
S.F.Singleton
(2007).
Inhibition of Escherichia coli RecA by rationally redesigned N-terminal helix.
|
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Org Biomol Chem,
5,
1525-1528.
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J.A.Parsons,
T.L.Bannam,
R.J.Devenish,
and
J.I.Rood
(2007).
TcpA, an FtsK/SpoIIIE homolog, is essential for transfer of the conjugative plasmid pCW3 in Clostridium perfringens.
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J Bacteriol,
189,
7782-7790.
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J.L.Mendoza,
and
P.J.Thomas
(2007).
Building an understanding of cystic fibrosis on the foundation of ABC transporter structures.
|
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J Bioenerg Biomembr,
39,
499-505.
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K.Okoshi,
T.Nishinaka,
Y.Doi,
R.Hara,
M.Hashimoto,
and
E.Yashima
(2007).
Liquid crystal formation of RecA-DNA filamentous complexes.
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Chem Commun (Camb),
(),
2022-2024.
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L.A.Bannister,
R.J.Pezza,
J.R.Donaldson,
D.G.de Rooij,
K.J.Schimenti,
R.D.Camerini-Otero,
and
J.C.Schimenti
(2007).
A dominant, recombination-defective allele of Dmc1 causing male-specific sterility.
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PLoS Biol,
5,
e105.
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L.T.Chen,
T.P.Ko,
Y.C.Chang,
K.A.Lin,
C.S.Chang,
A.H.Wang,
and
T.F.Wang
(2007).
Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins.
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Nucleic Acids Res,
35,
1787-1801.
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PDB code:
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M.A.Abbani,
C.V.Papagiannis,
M.D.Sam,
D.Cascio,
R.C.Johnson,
and
R.T.Clubb
(2007).
Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly.
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Proc Natl Acad Sci U S A,
104,
2109-2114.
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PDB code:
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M.M.Cox
(2007).
Motoring along with the bacterial RecA protein.
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Nat Rev Mol Cell Biol,
8,
127-138.
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O.R.Davies,
and
L.Pellegrini
(2007).
Interaction with the BRCA2 C terminus protects RAD51-DNA filaments from disassembly by BRC repeats.
|
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Nat Struct Mol Biol,
14,
475-483.
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R.C.Centore,
and
S.J.Sandler
(2007).
UvrD limits the number and intensities of RecA-green fluorescent protein structures in Escherichia coli K-12.
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J Bacteriol,
189,
2915-2920.
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R.L.Barnes,
and
R.McCulloch
(2007).
Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases.
|
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Nucleic Acids Res,
35,
3478-3493.
|
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S.Bailey,
W.K.Eliason,
and
T.A.Steitz
(2007).
The crystal structure of the Thermus aquaticus DnaB helicase monomer.
|
| |
Nucleic Acids Res,
35,
4728-4736.
|
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PDB code:
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T.H.Hazen,
D.Wu,
J.A.Eisen,
and
P.A.Sobecky
(2007).
Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp.
|
| |
Appl Environ Microbiol,
73,
7703-7710.
|
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T.Nishiwaki,
Y.Satomi,
Y.Kitayama,
K.Terauchi,
R.Kiyohara,
T.Takao,
and
T.Kondo
(2007).
A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria.
|
| |
EMBO J,
26,
4029-4037.
|
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V.G.Godoy,
D.F.Jarosz,
S.M.Simon,
A.Abyzov,
V.Ilyin,
and
G.C.Walker
(2007).
UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.
|
| |
Mol Cell,
28,
1058-1070.
|
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C.Joo,
S.A.McKinney,
M.Nakamura,
I.Rasnik,
S.Myong,
and
T.Ha
(2006).
Real-time observation of RecA filament dynamics with single monomer resolution.
|
| |
Cell,
126,
515-527.
|
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C.Wiese,
J.M.Hinz,
R.S.Tebbs,
P.B.Nham,
S.S.Urbin,
D.W.Collins,
L.H.Thompson,
and
D.Schild
(2006).
Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination.
|
| |
Nucleic Acids Res,
34,
2833-2843.
|
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|
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C.Wyman
(2006).
Monomer networking activates recombinases.
|
| |
Structure,
14,
949-950.
|
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D.Keramisanou,
N.Biris,
I.Gelis,
G.Sianidis,
S.Karamanou,
A.Economou,
and
C.G.Kalodimos
(2006).
Disorder-order folding transitions underlie catalysis in the helicase motor of SecA.
|
| |
Nat Struct Mol Biol,
13,
594-602.
|
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D.M.Baitin,
I.V.Bakhlanova,
Y.V.Kil,
M.M.Cox,
and
V.A.Lanzov
(2006).
Distinguishing characteristics of hyperrecombinogenic RecA protein from Pseudomonas aeruginosa acting in Escherichia coli.
|
| |
J Bacteriol,
188,
5812-5820.
|
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E.H.Egelman
(2006).
RecA assembly, one molecule at a time.
|
| |
Structure,
14,
1600-1602.
|
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G.Meinke,
P.A.Bullock,
and
A.Bohm
(2006).
Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
|
| |
J Virol,
80,
4304-4312.
|
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PDB code:
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J.M.Cox,
S.N.Abbott,
S.Chitteni-Pattu,
R.B.Inman,
and
M.M.Cox
(2006).
Complementation of one RecA protein point mutation by another. Evidence for trans catalysis of ATP hydrolysis.
|
| |
J Biol Chem,
281,
12968-12975.
|
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M.J.Bennett,
M.R.Sawaya,
and
D.Eisenberg
(2006).
Deposition diseases and 3D domain swapping.
|
| |
Structure,
14,
811-824.
|
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M.P.Killoran,
and
J.L.Keck
(2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
|
| |
Nucleic Acids Res,
34,
4098-4105.
|
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|
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M.Petukhov,
D.Lebedev,
V.Shalguev,
A.Islamov,
A.Kuklin,
V.Lanzov,
and
V.Isaev-Ivanov
(2006).
Conformational flexibility of RecA protein filament: transitions between compressed and stretched states.
|
| |
Proteins,
65,
296-304.
|
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|
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M.Spies,
and
S.C.Kowalczykowski
(2006).
The RecA binding locus of RecBCD is a general domain for recruitment of DNA strand exchange proteins.
|
| |
Mol Cell,
21,
573-580.
|
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|
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N.Sarai,
W.Kagawa,
T.Kinebuchi,
A.Kagawa,
K.Tanaka,
K.Miyagawa,
S.Ikawa,
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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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