5DDG

The structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with target double strand DNA

5DDG の概要

• エントリーDOI: 10.2210/pdb5ddg/pdb
• 関連するPDBエントリー: 5DD4
• 分子名称: transcriptional factor AraR, DNA (27-MER), MALONIC ACID, ... (6 entities in total)
• 機能のキーワード: structural genomics, psi-biology, midwest center for structural genomics, mcsg, arar, dna binding, transcriptional regulator, bacteroides thetaiotaomicron, helix-turn-helix motif, nudix fold, transcription regulator-dna complex, transcription regulator/dna
• 由来する生物種: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 70135.18

構造登録者

Chang, C.,Tesar, C.,Rodionov, D.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG) (登録日: 2015-08-24, 公開日: 2015-09-09, 最終更新日: 2015-12-16)

主引用文献

Chang, C.,Tesar, C.,Li, X.,Kim, Y.,Rodionov, D.A.,Joachimiak, A.
A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.
Nucleic Acids Res., 43:10546-10559, 2015

PubMed Abstract: Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.

PubMed: 26438537
DOI: 10.1093/nar/gkv1005

実験手法

X-RAY DIFFRACTION (3.06 Å)