Crystal structure of the single-stranded dna-binding protein from mycobacterium tuberculosis [unknown]

K. Saikrishnan, J. Jeyakanthan, J. Venkatesh, N. Acharya, K. Sekar, U. Varshney, M. Vijayan
2004 unpublished
bZIP) DNA-binding proteins play key roles in regulating gene transcription. Their DNA binding domains consist of the basic region juxtaposed to a heptad repeats of leucines. bZIP proteins from the same family recognize a unique palindromic DNA motif. bZIP peptide binds to DNA as a dimer of α helices. Dimerization is mediated by the leucine zipper; each basic region contacts a half-site in the major groove of the DNA. We solved the crystal structure of the C/EBPα bZIP peptide bound to a 21-mer
more » ... bound to a 21-mer DNA duplex. The current R-factor is 22.42% (R-free is 28.06%) in the 40 to 2.8 Å resolution range. Residues conserved among bZIP proteins -Asn292, Ala295 and Arg300 -make DNA contacts that are analogous to those observed in GCN4, CREB and Fos/Jun. Critical for the specific DNA binding by C/EBP proteins is the conformation of Arg289, which makes electrostatic interactions with Asn292, Asn293, and the adenine at position 3 (A3) in the consensus half-site (GCAAT). Val296 makes van der Waals contact with the methyl group of thymine which forms a base pair with A3. We also show that mutation of Arg289 to Ala completely abolishes the C/EBP α DNA binding, whereas a mutant in which Val296 is changed to Ala binds with comparable affinity to the C/EBP and CREB (halfsite = GTCAT) sites.
doi:10.2210/pdb1ue5/pdb fatcat:ey6uohbhingw3lg3eztczxy2e4