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

TY - JOUR

T1 - Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

AU - van Beest, M

AU - Dooijes, D

AU - van De Wetering, M

AU - Kjaerulff, S

AU - Bonvin, A

AU - Nielsen, O

AU - Clevers, H

AU - Nielsen, Olaf

PY - 2000/9/1

Y1 - 2000/9/1

N2 - 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.

AB - 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.

KW - Amino Acid Sequence

KW - Base Sequence

KW - Binding Sites

KW - DNA

KW - DNA Footprinting

KW - DNA Methylation

KW - Fungal Proteins

KW - High Mobility Group Proteins

KW - Magnetic Resonance Spectroscopy

KW - Models, Molecular

KW - Molecular Sequence Data

KW - Protein Conformation

KW - Schizosaccharomyces pombe Proteins

KW - Sequence Homology, Amino Acid

KW - Transcription Factors

U2 - 10.1074/jbc.M004102200

DO - 10.1074/jbc.M004102200

M3 - Journal article

C2 - 10867006

SN - 0021-9258

VL - 275

SP - 27266

EP - 27273

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

IS - 35

ER -