Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.
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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Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA.
Gao
Y G
YG
Robinson
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H
Liaw
Y C
YC
Edmondson
S P
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Shriver
J W
JW
Wang
A H
AH
D000595:Amino Acid Sequence; D019843:Archaeal Proteins; D020137:Base Pair Mismatch / Q000235:genetics*; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D006860:Hydrogen Bonding; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D055672:Static Electricity; D016944:Sulfolobus / Q000737:chemistry*; D016945:Sulfolobus acidocaldarius / Q000737:chemistry; D014867:Water / Q000378:metabolism
D019843:Archaeal Proteins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D007364:Intercalating Agents; C093228:Sso7d protein, Sulfolobus; D014867:Water; C095116:Sac7 protein, Sulfolobus; D004247:DNA