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PDBsum entry 1xmv
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DNA binding protein
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PDB id
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1xmv
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
43:16142-16152
(2004)
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PubMed id:
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Crystal structures of Escherichia coli RecA in complex with MgADP and MnAMP-PNP.
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X.Xing,
C.E.Bell.
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ABSTRACT
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RecA catalyzes the DNA pairing and strand-exchange steps of homologous
recombination, an important mechanism for repair of double-stranded DNA breaks.
The binding of RecA to DNA is modulated by adenosine nucleotides. ATP increases
the affinity of RecA for DNA, while ADP decreases the affinity. Previously, the
crystal structures of E. coli RecA and its complex with ADP have been determined
to resolutions of 2.3 and 3.0 A, respectively, but the model for the RecA-ADP
complex did not include magnesium ion or side chains. Here, we have determined
the crystal structures of RecA in complex with MgADP and MnAMP-PNP, a
nonhydrolyzable analogue of ATP, at resolutions of 1.9 and 2.1 A, respectively.
Both crystals grow in the same conditions and have RecA in a right-handed
helical form with a pitch of approximately 82 A. The crystal structures show the
detailed interactions of RecA with the nucleotide cofactors, including the metal
ion and the gamma phosphate of AMP-PNP. There are very few conformational
differences between the structures of RecA bound to ADP and AMP-PNP, which
differ from uncomplexed RecA only in a slight opening of the P-loop residues
66-73 upon nucleotide binding. To interpret the functional significance of the
structure of the MnAMP-PNP complex, a coprotease assay was used to compare the
ability of different nucleotides to promote the active, extended conformation of
RecA. Whereas ATPgammaS and ADP-AlF(4) facilitate a robust coprotease activity,
ADP and AMP-PNP do not activate RecA at all. We conclude that the crystal
structure of the RecA-MnAMP-PNP complex represents a preisomerization state of
the RecA protein that exists after ATP has bound but before the conformational
transition to the active state.
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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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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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M.Rusu,
and
S.Birmanns
(2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
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J Struct Biol,
170,
164-171.
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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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G.Walia,
P.Kumar,
and
A.Surolia
(2009).
The role of UPF0157 in the folding of M. tuberculosis dephosphocoenzyme A kinase and the regulation of the latter by CTP.
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PLoS One,
4,
e7645.
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J.N.Farb,
and
S.W.Morrical
(2009).
Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.
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J Mol Biol,
385,
393-404.
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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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J.Petersen,
C.J.Mitchell,
K.Fisher,
and
D.J.Lowe
(2008).
Structural basis for VO(2+)-inhibition of nitrogenase activity: (B) pH-sensitive inner-sphere rearrangements in the 1H-environment of the metal coordination site of the nitrogenase Fe-protein identified by ENDOR spectroscopy.
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J Biol Inorg Chem,
13,
637-650.
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H.Qiu,
and
Y.Wang
(2007).
Probing adenosine nucleotide-binding proteins with an affinity-labeled nucleotide probe and mass spectrometry.
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Anal Chem,
79,
5547-5556.
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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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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.
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Nat Struct Mol Biol,
13,
594-602.
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R.Krishna,
G.P.Manjunath,
P.Kumar,
A.Surolia,
N.R.Chandra,
K.Muniyappa,
and
M.Vijayan
(2006).
Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery.
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Nucleic Acids Res,
34,
2186-2195.
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PDB code:
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V.E.Galkin,
Y.Wu,
X.P.Zhang,
X.Qian,
Y.He,
X.Yu,
W.D.Heyer,
Y.Luo,
and
E.H.Egelman
(2006).
The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity.
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Structure,
14,
983-992.
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PDB code:
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C.E.Bell
(2005).
Structure and mechanism of Escherichia coli RecA ATPase.
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Mol Microbiol,
58,
358-366.
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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
codes are
shown on the right.
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Links
