title: Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.
abstract: 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.
authors.affiliation: Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA.
authors.forename: S
authors.initials: S
authors.lastname: Su
authors.forename: Y G
authors.initials: YG
authors.lastname: Gao
authors.forename: H
authors.initials: H
authors.lastname: Robinson
authors.forename: Y C
authors.initials: YC
authors.lastname: Liaw
authors.forename: S P
authors.initials: SP
authors.lastname: Edmondson
authors.forename: J W
authors.initials: JW
authors.lastname: Shriver
authors.forename: A H
authors.initials: AH
authors.lastname: Wang
mesh_terms: 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
chemical_list: 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