DNA-binding surface of the Sso7d protein from Sulfolobus solfataricus.
We have used nuclear magnetic resonance (n.m.r.) spectroscopy to identify the DNA-binding surface of the abundant, small and basic protein Sso7d from the hyperthermophilic archaebacterium Sulfolobus solfataricus. The Sso7d protein was previously found to bind strongly to double-stranded DNA sequences and to protect DNA from thermal denaturation, indicating that it might assume a similar function in vivo. Several amide resonances in two-dimensional n.m.r. 1H, 15N correlation spectra of 15N-enriched Sso7d are shifted and broadened upon addition of small amounts of ten base-pair or 19 base-pair duplex DNA oligomers under conditions where Sso7d-DNA complexes exchange rapidly on the n.m.r. time scale. The locations of the corresponding amides in the Sso7d structure define the surface that interacts with DNA. This surface coincides with a continuous region of strong positive electrostatic potential, which was calculated by means of numerical solution of the Poisson-Boltzmann equation. A model of the non-specific Sso7d-DNA complex is suggested based on the present data and previously obtained evidence that Sso7d interacts with the DNA major groove. The protein-DNA interface consists of a triple-stranded beta-sheet, which interacts with the DNA major groove and a reverse turn connecting the two strands of a double-stranded beta-sheet, which interacts with the minor groove. We note that the five (of 14) lysine side-chains that are specifically subjected to N zeta-monomethylation in the cell are located on surfaces of Sso7d that are exposed to the solvent in the proposed Sso7d-DNA complex.
Baumann
H
H
Center for Structural Biochemistry, Karolinska Institutet, Novum, Huddinge, Sweden.
Knapp
S
S
Karshikoff
A
A
Ladenstein
R
R
Härd
T
T
D019843:Archaeal Proteins; D001483:Base Sequence; D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D016944:Sulfolobus / Q000737:chemistry*; D013499:Surface Properties
D019843:Archaeal Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C093228:Sso7d protein, Sulfolobus