Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs.
Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment of promoter elements controlled by the yeast genes ste11 and Rox1 has indicated strict conservation of a larger DNA motif. By site selection, we identify a highly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we show that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12, 12, and 10 base pairs, respectively. Footprinting with a deletion mutant of Ste11 reveals a novel interaction between the 3' base pairs of the extended DNA motif and amino acids C-terminal to the HMG domain. The sequence-specific interaction of Ste11 with these 3' base pairs contributes significantly to binding and bending of the DNA motif.
van Beest
M
M
Department of Immunology, University Medical Center Utrecht, Heidelberglaan 100 Rm F03.821, 3584 CX Utrecht, The Netherlands.
Dooijes
D
D
van De Wetering
M
M
Kjaerulff
S
S
Bonvin
A
A
Nielsen
O
O
Clevers
H
H
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D018983:DNA Footprinting; D019175:DNA Methylation; D005656:Fungal Proteins / Q000378:metabolism; D006609:High Mobility Group Proteins / Q000737:chemistry / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D029702:Schizosaccharomyces pombe Proteins; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000378:metabolism
D005656:Fungal Proteins; D006609:High Mobility Group Proteins; D029702:Schizosaccharomyces pombe Proteins; D014157:Transcription Factors; C071596:ste11 protein, S pombe; D004247:DNA