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PDBsum entry 1ca5
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Structural protein/DNA
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PDB id
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1ca5
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DOI no:
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J Mol Biol
303:395-403
(2000)
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PubMed id:
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Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.
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S.Su,
Y.G.Gao,
H.Robinson,
Y.C.Liaw,
S.P.Edmondson,
J.W.Shriver,
A.H.Wang.
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ABSTRACT
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Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic
archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius,
respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and
Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A,
respectively, to investigate the DNA binding property of Sso7d/Sac7d in the
presence of a T-G mismatch base-pair. Detailed structural analysis revealed that
the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind
to that mismatch base-pair in a manner similar to regular DNA. In the
Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4
is formed and well-order bridging water molecules are found. The results suggest
that the less stable DNA stacking site involving a T-G mismatch may be a
preferred site for protein side-chain intercalation.
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Selected figure(s)
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Figure 3.
Figure 3. The r.m.s.d. statistics of for each residue in
the seven structures shown in Figure 2 are shown for the
main-chains and the side-chains.
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Figure 4.
Figure 4. (a) Superposition of DNA intercalation sites for
four Sso7d/Sac7d-DNA complexes: Sso7d-GCGATCGC, Sso7d-GTGATCGC,
Sso7d-GTAATTAC and Sac7d-GTAATTAC. The models are fitted by the
common backbone atoms of protein. (b) The schematic diagram of
the DNA backbone conformation in Sso7d-GTGATCGC. The sugars
around the intercalation site adopt C3'-endo (N-type) pucker,
similar to A-DNA conformation. The right panel shows the
intercalation site of DNA, fitted to A-DNA using base-pair atoms.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
303,
395-403)
copyright 2000.
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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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F.Paquet,
K.Loth,
H.Meudal,
F.Culard,
D.Genest,
and
G.Lancelot
(2010).
Refined solution structure and backbone dynamics of the archaeal MC1 protein.
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FEBS J,
277,
5133-5145.
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PDB code:
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S.Haider,
G.N.Parkinson,
and
S.Neidle
(2008).
Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.
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Biophys J,
95,
296-311.
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A.Korostelev,
S.Trakhanov,
H.Asahara,
M.Laurberg,
L.Lancaster,
and
H.F.Noller
(2007).
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
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Proc Natl Acad Sci U S A,
104,
16840-16843.
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PDB codes:
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B.Mouratou,
F.Schaeffer,
I.Guilvout,
D.Tello-Manigne,
A.P.Pugsley,
P.M.Alzari,
and
F.Pecorari
(2007).
Remodeling a DNA-binding protein as a specific in vivo inhibitor of bacterial secretin PulD.
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Proc Natl Acad Sci U S A,
104,
17983-17988.
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D.T.Mackay,
C.H.Botting,
G.L.Taylor,
and
M.F.White
(2007).
An acetylase with relaxed specificity catalyses protein N-terminal acetylation in Sulfolobus solfataricus.
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Mol Microbiol,
64,
1540-1548.
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C.Y.Chen,
T.P.Ko,
T.W.Lin,
C.C.Chou,
C.J.Chen,
and
A.H.Wang
(2005).
Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d.
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Nucleic Acids Res,
33,
430-438.
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PDB codes:
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A.Merlino,
G.Graziano,
and
L.Mazzarella
(2004).
Structural and dynamic effects of alpha-helix deletion in Sso7d: implications for protein thermal stability.
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Proteins,
57,
692-701.
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T.P.Ko,
H.M.Chu,
C.Y.Chen,
C.C.Chou,
and
A.H.Wang
(2004).
Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.
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Acta Crystallogr D Biol Crystallogr,
60,
1381-1387.
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PDB codes:
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D.Serban,
J.M.Benevides,
and
G.J.Thomas
(2003).
HU protein employs similar mechanisms of minor-groove recognition in binding to different B-DNA sites: demonstration by Raman spectroscopy.
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Biochemistry,
42,
7390-7399.
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J.N.Reeve
(2003).
Archaeal chromatin and transcription.
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Mol Microbiol,
48,
587-598.
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S.Maurer-Stroh,
N.J.Dickens,
L.Hughes-Davies,
T.Kouzarides,
F.Eisenhaber,
and
C.P.Ponting
(2003).
The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains.
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Trends Biochem Sci,
28,
69-74.
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M.H.Hou,
S.B.Lin,
J.M.Yuann,
W.C.Lin,
A.H.Wang,
and
L.Kan Ls
(2001).
Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure.
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Nucleic Acids Res,
29,
5121-5128.
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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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