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PDBsum entry 1c8c
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DNA binding protein/DNA
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PDB id
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1c8c
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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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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Authors
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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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Ref.
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J Mol Biol, 2000,
303,
395-403.
[DOI no: ]
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PubMed id
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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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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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