Solution structure and DNA binding property of the fifth HMG box domain in comparison with the first HMG box domain in human upstream binding factor

Human upstream binding factor (hUBF) is a nucleolar transcription factor involved in transcription by RNA polymerase I. It contains six HMG box domains. The contribution of each HMG box motif to its function is different. hUBF HMG box 1 shows a very strong binding affinity for both the four-way DNA junction and a 15 bp GC-rich rRNA gene core promoter fragment, but hUBF HMG box 5 shows a much weaker binding affinity for the four-way DNA junction and the GC-rich rRNA gene core promoter fragment. To illustrate the molecular basis of their DNA binding difference, the solution structure of box 5 was studied by NMR. The tertiary structure of box 5 shows a common flattened L-shaped fold, similar to box I and other HMG boxes with known structures. It is formed by intersection of three helical arms: helix I (residues 9-25) and helix 2 (residues 30-42) pack into each other to form the major wing, while helix 3 (residues 48-70) is aligned with the extended N-terminal segment to form the minor wing. A hydrophobic core is formed by three tryptophans (W14, W41, and W52) to maintain the fold. Although there is similarity between the two structures, negative charged electrostatic surface potential in the concave face of the molecule of box 5 exhibits great difference compared to that of box 1 and other HMG boxes with known structures. That surface is involved in DNA binding. Besides, in positions which are involved in intercalating into a DNA base pair, there are hydrophobic residues in box 1 and other HMG boxes but polar residues in box 5. These differences may contribute to the loss of the DNA binding ability of box 5.