5bpd

Publication Abstract from PubMed

The crystal structure of TrmBL2 from the archaeon P. furiosus shows an association of two pseudo-symmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix domains binding to successive major grooves of the DNA. However, in TrmBL2 the two dimers are arranged at a mutual displacement of approximately two base pairs so that they associate with the DNA along the double helical axis at an angle of approximately 80 degrees . While the deoxyribose phosphate groups of the dsDNA used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The helix-turn-helix domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seem to arise from non-optimal protein-DNA contacts made by its four helix-turn-helix domains resulting in a low-affinity, nonspecific binding to DNA.

Structural insights into nonspecific binding of DNA by TrmBL2, an archaeal chromatin protein.,Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W J Mol Biol. 2015 Aug 20. pii: S0022-2836(15)00458-1. doi:, 10.1016/j.jmb.2015.08.012. PMID:26299937^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.