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Protein Science, Vol 3, Issue 10 1806-1821, Copyright © 1994 by Cold Spring Harbor Laboratory Press

ARTICLE

Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy

F. F. DAMBERGER, J. G. PELTON, C. J. HARRISON, HCM. NELSON and D. E. WEMMER
Biophysics Graduate Group, University of California, Berkeley, California 94720

The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, (1)H-(13)C-(13)C-(1)H total correlation spectroscopy, and (15)N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain (1)H, (15)N, and (13)C resonances. Five-hundred eighty-three NOE constraints identified in 3D (13)C- and (15)N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional (13)C/(13)C-edited NOESY spectrum, along with 35 {phi}, 9 ({chi}1), and 30 hydrogen bond constraints, were used to calculate 30 structures by a hybrid distance geometry/simulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel {beta}-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal.
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