5BOX

Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.

5BOX の概要

• エントリーDOI: 10.2210/pdb5box/pdb
• 分子名称: Putative HTH-type transcriptional regulator TrmBL2, DNA TGM (25-MER), DNA (25-MER), ... (6 entities in total)
• 機能のキーワード: chromatin binding protein, dna binding protein
• 由来する生物種: Pyrococcus furiosus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 138434.72

構造登録者

Ahmad, M.U.,Diederichs, K.,Welte, W. (登録日: 2015-05-27, 公開日: 2015-09-02, 最終更新日: 2024-01-10)

主引用文献

Ahmad, M.U.,Waege, I.,Hausner, W.,Thomm, M.,Boos, W.,Diederichs, K.,Welte, W.
Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.
J.Mol.Biol., 427:3216-3229, 2015

PubMed Abstract: The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°. While the deoxyribose phosphate groups of the double-stranded DNA (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 HTH 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 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.

PubMed: 26299937
DOI: 10.1016/j.jmb.2015.08.012

実験手法

X-RAY DIFFRACTION (2.5 Å)