User:Cameron Ball/Sandbox 1: Difference between revisions

To arrest DNA replication, the two RTP dimers bind at a specific DNA site. These sites, designated ''Ter'' sites, are 29 base pairs in length and comprise of two non-identical inverted repeats that share three highly conserved base pairs. The two sites are designated the A-site and the B-site and each have different affinities for RTP (with the B-site exhibiting greater protein-DNA contact and thus greater affinity<ref>Langley, D. B., Smith, M. T., Lewis, P. J., and Wake, R. G. Protein-nucleoside contacts in the interaction between the replication terminator protein of Bacillus subtilis and the DNA terminator. (1993) Mol. Microbiol. 10, 771-779</ref>). It is now known that RTP binds to Ter site in a directional manner as a result of these non-identical sites, which plays an important role in allowing polymerase units to pass by one way but blocking them in another. However, historically, the exact way in which symmetric RTP dimers blocked polymerases in a polar fashion was a source of great confusion. This was compounded by the fact that a symmetrical DNA sequence (designated sRB) was used in the first crystal structure of an RTP:DNA complex. <ref>Wilce, J. A., Vivian, J. P., Hastings, A. F., Otting, G., Folmer, R. H., Duggin, I. G., Wake, R. G. & Wilce, M. C., Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest., (2001). Nature Struct. Biol.8, 206–210.</ref>

<scene name='User:Cameron_Ball/Sandbox_1/Rtp_dna_complex/1'>RTP binds DNA</scene> through interactions between the <scene name='User:Cameron_Ball/Sandbox_1/Rtp_alpha_helices_and_dna_/4'>alpha helices</scene> and the major groove of DNA. The first crystal structure of RTP complexed to the native TerB site (nRB) was solved by vivian ''et al'' in 2007<ref>J.P. Vivian, C.J. Porter, J.A. Wilce, M.C.J. Wilce, An Asymmetric Structure of the Bacillus subtilis Replication Terminator Protein in Complex with DNA, Journal of Molecular Biology, Volume 370, Issue 3, 13 July 2007, Pages 481-491, ISSN 0022-2836, DOI: 10.1016/j.jmb.2007.02.067.</ref>. The induced asymmetry of the RTP dimer results in a <scene name='User:Cameron_Ball/Sandbox_1/Wing_up_turn/3'>wing up</scene> and a <scene name='User:Cameron_Ball/Sandbox_1/Wing_down_turn/4'>wing down</scene> beta loop turn.