Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by nmr spectroscopy

R. Boelens, H. Vis, C.E. Vorgias, K.S. Wilson, R. Kaptein

Research output: Contribution to journalArticleAcademicpeer-review


The DNA-binding protein HU from Bacillus stearothermophilus (HUBst) is a dimer with a molecular weight of 19.5 kDa that is capable of bending DNA. An x-ray structure has been determined previously [Tanaka et al. (1984) Nature, Vol. 310, pp. 376-381], but no structure could be established for a large part of the supposed DNA-binding β-arms. Distance geometry and restrained molecular dynamics using nmr restraints were used to generate a set of 25 structures. These structures display a backbone rms deviation (RMSD) of 0.36 Å for the well-defined region (residues 2-54 and 75-90). The structure of the core is very similar to that observed in the x-ray structure, with a pairwise RMSD of 1.06 Å. The structure of the β-hairpin arm contains a double flip-over at the prolines in the two strands of the β-arm. Heteronuclear15N relaxation measurements indicate that the β-arm and the tip of the β-arm is flexible. This explains the disorder observed in the solution and x-ray structures of the β-arm with respect to the core of the protein. Overlayed onto itself the β-arm is better defined, with an backbone RMSD of 1.0 Å calculated for residues 54-59 and 69-74. The tip of the arm adopts a well-defined 4 : 6 β-hairpin conformation. Changes in amide15N and1H chemical shifts upon titrating DNA are most pronounced for the residues in the β-hairpin arm and for the residues in the second half of the third α-helix. Heteronuclear15N relaxation data for free and complexed HUBst show that the arms become structured upon DNA binding. Together with chemically induced nuclear polarization measurements on a mutant HUBst (M69Y; V76Y) this straws that the β-hairpin arm is involved in direct DNA interaction.
Original languageEnglish
Pages (from-to)553-559
Number of pages7
Issue number5
Publication statusPublished - 8 Sept 1996


  • heteronuclear relaxation measurements
  • photo-CIDNP
  • protein dynamics
  • protein structure
  • protein-DNA complex
  • triple-resonance nmr
  • DNA binding protein
  • article
  • Geobacillus stearothermophilus
  • molecular dynamics
  • nonhuman
  • nuclear magnetic resonance spectroscopy
  • protein DNA binding


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