Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius.
The Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius are a heterogeneous mixture of small, thermostable, nonspecific DNA-binding proteins. One of these proteins, Sac7d, has been overexpressed in Escherichia coli to provide a homogeneous preparation for structure, stability, and function studies. We present here essentially complete sequence-specific 1H NMR assignments for Sac7d, a delineation of secondary structural elements, and the high-resolution solution structure obtained from a full relaxation matrix refinement. The final structure provides an excellent fit to the NMR data with an NOE R-factor of 0.27 for backbone NOEs. The structure has a compact globular fold with 82% of the sequence involved in regular secondary structure: an antiparallel two-stranded beta-ribbon with a tight turn, followed by a short 3(10) helix, an antiparallel three-stranded beta-sheet, another short 3(10) helix, and finally four turns of alpha-helix. The amphipathic alpha-helix packs across the hydrophobic face of the three-stranded beta-sheet in an open-faced sandwich arrangement with at least one turn of the helix exposed beyond the sheet. The hydrophobic face of the beta-ribbon packs against a corner of the twisted beta-sheet. The single tryptophan responsible for the 88% fluorescence quenching upon DNA binding is exposed on the surface of the three-stranded beta-sheet. Lysines 5 and 7, whose monomethylation may be associated with enhanced thermostability, are highly solvent exposed along the inner edge of the two-stranded ribbon. The structure of Sac7d differs in many respects from that reported for the homologous native Sso7d [Baumann et al. (1994) Nature Struct. Biol. 1, 808] with a backbone RMSD greater than 3.0 A, largely due to the packing and length of the C-terminal alpha-helix which may be important in Sac7d DNA binding.
Edmondson
S P
SP
Department of Medical Biochemistry, School of Medicine, Southern Illinois University, Carbondale 62901, USA.
Qiu
L
L
Shriver
J W
JW
D000595:Amino Acid Sequence; D019843:Archaeal Proteins; D001426:Bacterial Proteins / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006358:Hot Temperature; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry; D012996:Solutions; D016945:Sulfolobus acidocaldarius / Q000378:metabolism*
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D011994:Recombinant Proteins; D012996:Solutions; C095116:Sac7 protein, Sulfolobus; D004247:DNA