A refined solution structure of the glucocorticoid receptor DNA-binding domain (GR DBD) has been determined using two- and three-dimensional nuclear magnetic resonance (NMR) spectroscopy on an 15N-labeled GR DBD fragment in conjunction with distance geometry and simulated annealing calculations. Thirty structures of the fragment C440-R510 of the rat GR were calculated based on 906 distance constraints obtained from NOE intensities (168 intraresidue and 738 interresidue NOEs) and 43 dihedral constraints. Average atomic root mean square (rms) differences between the 24 best structures and their geometric average are 0.70 Å for backbone atoms and 1.44 Å for all heavy atoms. Several regions that were not well defined in a previous NMR structure determination of a similar protein fragment [Hard, T., Kellenbach, E., Boelens, R., Maler, B. A., Dahlman, K., Freedman, L. P., Carlstedt-Duke, J., Yamamoto, K. R., Gustafsson, J.-A., and Kaptein, R. (1990b) Science 249, 157-160] are now well-defined. The refined structure of the uncomplexed GR DBD is very similar to the crystal structure of GR DBD in a sequence specific DNA complex [Luisi, B. F., Xu, W. X., Otwinowski, Z., Freedman, L. P., Yamamoto, K. R., and Sigler, P. B. (1991) Nature 352, 497-505], in particular with regard to the presence and relative positions of secondary structure elements. The backbone atom rms difference between the average NMR solution structure and the crystal structure of the DNA-complexed GR DBD is 1.8 Å. The most pronounced differences between the free and DNA-complexed states are found within the fragment C476-C482 in the second zinc-coordinating domain. The different conformations of this fragment, which includes the so-called D- box, can be rationalized in terms of conformational changes induced by protein-protein interactions upon formation of a dimeric DBD-DNA complex.
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