Structure of the HMG box motif in the B‐domain of HMG1.

The conserved, abundant chromosomal protein HMG1 consists of two highly homologous, folded, basic DNA‐binding domains, each of approximately 80 amino acid residues, and an acidic C‐terminal tail. Each folded domain represents an ‘HMG box’, a sequence motif recently recognized in certain sequence‐specific DNA‐binding proteins and which also occurs in abundant HMG1‐like proteins that bind to DNA without sequence specificity. The HMG box is defined by a set of highly conserved residues (most distinctively aromatic and basic) and appears to define a novel DNA‐binding structural motif. We have expressed the HMG box region of the B‐domain of rat HMG1 (residues 88–164 of the intact protein) in Escherichia coli and we describe here the determination of its structure by 2D 1H‐NMR spectroscopy. There are three alpha‐helices (residues 13–29, 34–48 and 50–74), which together account for approximately 75% of the total residues and contain many of the conserved basic and aromatic residues. Strikingly, the molecule is L‐shaped, the angle of approximately 80 degrees between the two arms being defined by a cluster of conserved, predominantly aromatic, residues. The distinctive shape of the HMG box motif, which is distinct from hitherto characterized DNA‐binding motifs, may be significant in relation to its recognition of four‐way DNA junctions.