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J Biol Chem. 2000 Sep 1;275(35):27266-73.

Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs.

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1
Department of Immunology, University Medical Center Utrecht, Heidelberglaan 100 Rm F03.821, 3584 CX Utrecht, The Netherlands.

Abstract

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.

PMID:
10867006
DOI:
10.1074/jbc.M004102200
[Indexed for MEDLINE]
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