7P3F

Streptomyces coelicolor dATP/ATP-loaded NrdR in complex with its cognate DNA

7P3F の概要

• エントリーDOI: 10.2210/pdb7p3f/pdb
• 関連するPDBエントリー: 7P37 7P3Q
• EMDBエントリー: 13179
• 分子名称: Transcriptional repressor NrdR, DNA (50-MER), ADENOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• 機能のキーワード: repressor, dodecamer, atp-binding, datp-binding, dna binding protein
• 由来する生物種: Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 124476.07

構造登録者

Martinez-Carranza, M.,Stenmark, P. (登録日: 2021-07-07, 公開日: 2022-05-11, 最終更新日: 2024-07-17)

主引用文献

Rozman Grinberg, I.,Martinez-Carranza, M.,Bimai, O.,Nouairia, G.,Shahid, S.,Lundin, D.,Logan, D.T.,Sjoberg, B.M.,Stenmark, P.
A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases.
Nat Commun, 13:2700-2700, 2022

PubMed Abstract: Ribonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria - including well-known pathogens such as Mycobacterium tuberculosis - NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.

PubMed: 35577776
DOI: 10.1038/s41467-022-30328-1

実験手法

ELECTRON MICROSCOPY (3.31 Å)