3N97

RNA polymerase alpha C-terminal domain (E. coli) and sigma region 4 (T. aq. mutant) bound to (UP,-35 element) DNA

3N97 の概要

• エントリーDOI: 10.2210/pdb3n97/pdb
• 関連するPDBエントリー: 3K4G 3N4M
• 分子名称: RNA polymerase sigma factor, DNA-directed RNA polymerase subunit alpha, DNA (5'-D(*TP*GP*GP*AP*AP*AP*AP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*CP*AP*TP*GP*G)-3'), ... (6 entities in total)
• 機能のキーワード: protein-protein interactions, protein-dna interactions, transcription initiation, gene regulation-dna complex, gene regulation/dna
• 由来する生物種: Thermus aquaticus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 49031.93

構造登録者

Lara-Gonzalez, S.,Birktoft, J.J.,Lawson, C.L. (登録日: 2010-05-28, 公開日: 2011-06-08, 最終更新日: 2023-09-06)

主引用文献

Lara-Gonzalez, S.,Dantas Machado, A.C.,Rao, S.,Napoli, A.A.,Birktoft, J.,Di Felice, R.,Rohs, R.,Lawson, C.L.
The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element.
Biochemistry, 59:4523-4532, 2020

PubMed Abstract: We demonstrate here that the α subunit C-terminal domain of RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of αCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A-tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A-tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A-tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second αCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either αCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving αCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors.

PubMed: 33205945
DOI: 10.1021/acs.biochem.0c00571

実験手法

X-RAY DIFFRACTION (3.252 Å)