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PDBsum entry 1i1v
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Deoxyribonucleic acid
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PDB id
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1i1v
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References listed in PDB file
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Key reference
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Title
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Base pair switching by interconversion of sugar puckers in DNA extended by proteins of reca-Family: a model for homology search in homologous genetic recombination.
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Authors
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T.Nishinaka,
A.Shinohara,
Y.Ito,
S.Yokoyama,
T.Shibata.
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Ref.
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Proc Natl Acad Sci U S A, 1998,
95,
11071-11076.
[DOI no: ]
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PubMed id
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Abstract
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Escherichia coli RecA is a representative of proteins from the RecA family,
which promote homologous pairing and strand exchange between double-stranded DNA
and single-stranded DNA. These reactions are essential for homologous genetic
recombination in various organisms. From NMR studies, we previously reported a
novel deoxyribose-base stacking interaction between adjacent residues on the
extended single-stranded DNA bound to RecA protein. In this study, we found that
the same DNA structure was induced by the binding to Saccharomyces cerevisiae
Rad51 protein, indicating that the unique DNA structure induced by the binding
to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of
this structure, we have formulated the structure of duplex DNA within filaments
formed by RecA protein and its homologs. Two types of molecular structures are
presented. One is the duplex structure that has the N-type sugar pucker. Its
helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an
active, or ATP-form of the RecA filament. The other is one that has the S-type
sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn),
corresponding to that of an inactive, or ADP-form of the RecA filament. During
this modeling, we found that the interconversion of sugar puckers between the
N-type and the S-type rotates bases horizontally, while maintaining the
deoxyribose-base stacking interaction. We propose that this base rotation
enables base pair switching between double-stranded DNA and single-stranded DNA
to take place, facilitating homologous pairing and strand exchange. A possible
mechanism for strand exchange involving DNA rotation also is discussed.
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Figure 3.
Fig. 3. Base rotation by interconversion of sugar
puckers. (a) Top view of the base rotation caused by
interconversion of the sugar puckers. The sugar pucker of the
5'-residue (T, top) is in the S-type (Left) and the N-type
(Right), whereas that of the 3'-residue (A, bottom) is fixed in
the S-type. Note that the hydrogen-bonding vector is rotated
toward its major groove by the conversion from the S-type to the
N-type. (b) Two types of deoxyribose-base stacking. All residues
are in the S-type sugar pucker (Left) or the N-type (Right)
sugar pucker.
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Figure 4.
Fig. 4. A three-stranded DNA model for homology search
and strand exchange considering the N-S interconversion of sugar
puckers. (a) A molecular model of base pair switch between
single- and double-stranded DNA. The bottom three residues are
in the N-type and the top three residues are in the S-type. Note
that the base pairing is altered by the conversion of sugar
puckers between the N- and S-type. (b) Base rotation schemes for
base pair switching against the interconversion of the sugar
puckers. The bases are rotated toward the minor groove when the
sugar puckers are converted from the N-type (Left) to the S-type
(Right) and toward the major groove with the opposite (S-type to
N-type) conversion.
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