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PDBsum entry 1f0a
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Protein binding
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PDB id
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1f0a
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DOI no:
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Protein Sci
9:2161-2169
(2000)
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PubMed id:
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Solution structure of DinI provides insight into its mode of RecA inactivation.
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B.E.Ramirez,
O.N.Voloshin,
R.D.Camerini-Otero,
A.Bax.
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ABSTRACT
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The Escherichia coli RecA protein triggers both DNA repair and mutagenesis in a
process known as the SOS response. The 81-residue E. coli protein DinI inhibits
activity of RecA in vivo. The solution structure of DinI has been determined by
multidimensional triple resonance NMR spectroscopy, using restraints derived
from two sets of residual dipolar couplings, obtained in bicelle and phage
media, supplemented with J couplings and a moderate number of NOE restraints.
DinI has an alpha/beta fold comprised of a three-stranded beta-sheet and two
alpha-helices. The beta-sheet topology is unusual: the central strand is flanked
by a parallel and an antiparallel strand and the sheet is remarkably flat. The
structure of DinI shows that six negatively charged Glu and Asp residues on
DinI's kinked C-terminal alpha-helix form an extended, negatively charged ridge.
We propose that this ridge mimics the electrostatic character of the DNA
phospodiester backbone, thereby enabling DinI to compete with single-stranded
DNA for RecA binding. Biochemical data confirm that DinI is able to displace
ssDNA from RecA.
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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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V.E.Galkin,
R.L.Britt,
L.B.Bane,
X.Yu,
M.M.Cox,
and
E.H.Egelman
(2011).
Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein.
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J Mol Biol,
408,
815-824.
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Y.Shen,
and
A.Bax
(2010).
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network.
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J Biomol NMR,
48,
13-22.
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C.Y.Yang,
K.H.Chin,
M.T.Yang,
A.H.Wang,
and
S.H.Chou
(2009).
Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris.
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Proteins,
74,
530-537.
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PDB code:
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Y.Shen,
F.Delaglio,
G.Cornilescu,
and
A.Bax
(2009).
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.
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J Biomol NMR,
44,
213-223.
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J.E.Long,
N.Renzette,
R.C.Centore,
and
S.J.Sandler
(2008).
Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.
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PLoS ONE,
3,
e4100.
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G.B.Zavilgelsky,
and
S.M.Rastorguev
(2007).
DNA mimicry by proteins as effective mechanism for regulation of activity of DNA-dependent enzymes.
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Biochemistry (Mosc),
72,
913.
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N.Renzette,
N.Gumlaw,
and
S.J.Sandler
(2007).
DinI and RecX modulate RecA-DNA structures in Escherichia coli K-12.
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Mol Microbiol,
63,
103-115.
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D.T.Dryden
(2006).
DNA mimicry by proteins and the control of enzymatic activity on DNA.
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Trends Biotechnol,
24,
378-382.
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M.N.Triba,
D.E.Warschawski,
and
P.F.Devaux
(2005).
Reinvestigation by phosphorus NMR of lipid distribution in bicelles.
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Biophys J,
88,
1887-1901.
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M.Zweckstetter,
G.Hummer,
and
A.Bax
(2004).
Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases.
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Biophys J,
86,
3444-3460.
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S.R.Casjens,
E.B.Gilcrease,
W.M.Huang,
K.L.Bunny,
M.L.Pedulla,
M.E.Ford,
J.M.Houtz,
G.F.Hatfull,
and
R.W.Hendrix
(2004).
The pKO2 linear plasmid prophage of Klebsiella oxytoca.
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J Bacteriol,
186,
1818-1832.
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Y.Qu,
J.T.Guo,
V.Olman,
and
Y.Xu
(2004).
Protein structure prediction using sparse dipolar coupling data.
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Nucleic Acids Res,
32,
551-561.
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A.Bax
(2003).
Weak alignment offers new NMR opportunities to study protein structure and dynamics.
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Protein Sci,
12,
1.
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J.Meiler,
and
D.Baker
(2003).
Rapid protein fold determination using unassigned NMR data.
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Proc Natl Acad Sci U S A,
100,
15404-15409.
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R.Benton,
and
D.St Johnston
(2003).
A conserved oligomerization domain in drosophila Bazooka/PAR-3 is important for apical localization and epithelial polarity.
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Curr Biol,
13,
1330-1334.
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D.J.Crowley,
and
J.Courcelle
(2002).
Answering the Call: Coping with DNA Damage at the Most Inopportune Time.
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J Biomed Biotechnol,
2,
66-74.
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M.D.Walkinshaw,
P.Taylor,
S.S.Sturrock,
C.Atanasiu,
T.Berge,
R.M.Henderson,
J.M.Edwardson,
and
D.T.Dryden
(2002).
Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA.
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Mol Cell,
9,
187-194.
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PDB code:
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J.H.Prestegard,
and
A.I.Kishore
(2001).
Partial alignment of biomolecules: an aid to NMR characterization.
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Curr Opin Chem Biol,
5,
584-590.
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J.R.Tolman
(2001).
Dipolar couplings as a probe of molecular dynamics and structure in solution.
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Curr Opin Struct Biol,
11,
532-539.
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K.J.Glover,
J.A.Whiles,
G.Wu,
N.Yu,
R.Deems,
J.O.Struppe,
R.E.Stark,
E.A.Komives,
and
R.R.Vold
(2001).
Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules.
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Biophys J,
81,
2163-2171.
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O.N.Voloshin,
B.E.Ramirez,
A.Bax,
and
R.D.Camerini-Otero
(2001).
A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA.
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Genes Dev,
15,
415-427.
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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
