Solution structure of the HU protein from Bacillus stearothermophilus

H. Vis, M. Mariani, C.E. Vorglas, K.S. Wilson, R. Kaptein, R. Boelens

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

The histone-like protein HU from Bacillus stearothermophilus is a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding β-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a13C/15N doubly-labelled HU protein 49 distance geometry structures were calculated, which were refined by means of restrained Molecular Dynamics. From this set a total of 25 refined structures were selected having low constraint energy and few constraint violations. The ensemble of 25 structures display a root-mean-square co-ordinate deviation of 0.36 Å with respect to the average structure, calculated over the backbone heavy atoms of residues 2 to 54 and 75 to 90 (and residues 2' to 54' and 75' to 90' of the second monomer). The structure of the core is very similar to that observed in the X-ray structure, with a pairwise r.m.s.d. 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. Strong15N-NH heteronuclear nuclear Overhauser effects indicate that the β-arm and especially the tip is flexible. This explains the disorder observed in the solution and X-ray structures of the β-arm, in respect of the core of the protein. Overlayed onto itself the β-arm is better defined, with an r.m.s.d, of 1.0 Å, calculated over the backbone heavy atoms of residues 54 to 59 and 69 to 74. The tip of the arm adopts a well-defined 4:6 β-hairpin conformation similar to the iron co-ordinating β-arms of rubredoxin.
Original languageEnglish
Pages (from-to)692-703
Number of pages12
JournalJournal of Molecular Biology
Volume254
Issue number4
DOIs
Publication statusPublished - 8 Sept 1995

Keywords

  • β-turn
  • DNA-binding protein
  • Restrained molecular dynamics
  • Structure refinement
  • Triple-resonance NMR
  • bacterial protein
  • carbon 13
  • dimer
  • DNA binding protein
  • histone
  • nitrogen 15
  • article
  • Geobacillus stearothermophilus
  • isotope labeling
  • molecular dynamics
  • nonhuman
  • nuclear magnetic resonance
  • nuclear Overhauser effect
  • priority journal
  • protein structure
  • X ray analysis

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