An NMR study on the DNA-binding SPKK motif and a model for its interaction with DNA.
The solution structure of one and two repeats of the 'SPKK' DNA-binding motif is reported on the basis of NMR measurements. In dimethylsulphoxide (DMSO) the major population (approximately 90%) of peptides, SPRKSPRK(S2) and GSPKKSPRK(S2b), adopts a conformation, which has two trans prolines. The two 'SP(R/K)K' units in these peptides are equivalent and each adopts a turn structure exchanging with an extended structure. This is suggested by an NOE connectivity of the beta-turn type, between the backbone amide protons of residues (i+2) and (i+3) and NOE connectivities of the Asx(sigma)-turn type, between protons of the ith Ser and the backbone amide proton on residue (i+2). This suggests that each SP(R/K)K unit has a structural intermediate between (or a combination of) a beta-turn and an Asx(sigma)-turn. In 90-10% DMSO/H2O at 4 degrees C the two units of S2 are connected more tightly by folding into a short 3(10) helix, broken at the second proline. For another peptide, Thr-Pro-Arg-Lys(T1), the major population (75%) in 100% DMSO comprises a beta-turn in rapid exchange with an extended structure. We did not observe an NOE connectivity of the Asx(sigma) type with the T1 peptide. A possible structure of the SPKK motif in the complex with DNA is discussed.
Suzuki
M
M
MRC Laboratory of Molecular Biology, Cambridge, UK.
Gerstein
M
M
Johnson
T
T
D000595:Amino Acid Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010446:Peptide Fragments / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary
D004268:DNA-Binding Proteins; D010446:Peptide Fragments; D004247:DNA