DBD sequences encoded by C. elegans NR genes described in this study. Shaded amino acids are conserved in all NRs other than the nematode exceptions noted in the text.. Arrows indicate the eight zinc-coordinating cysteines (four per zinc-binding module). Asterisks denote positions of residues found to make specific DNA contacts in the existing NR DBD X-ray crystal structures (Rastinejad 1997). Underlying rectangles in the core DBD indicate the P box sequences that are primary determinants of DNA-binding specificity and the D box dimerization interface (Gronemeyer and Laudet 1995). Also indicated are the T box and A box regions that contribute to dimerization and DNA binding, respectively, by some NRs (Gronemeyer and Laudet 1995;Rastinejad 1997). Alignments were generated using the GCG Pileup program (Devereux et al. 1984). (A) NR sequences identified by degenerate PCR amplification of genomic DNA. Amino acids encoded by the original amplification products are underlined. (B) NR sequences identified from expressed sequence tags. The nhr-14DBD sequences are from the corresponding genome project ORF prediction, as the cDNA sequenced was incomplete and did not extend to the DBD region.
