Crystal structure of the full‐length LysR‐type transcription regulator CbnR in complex with promoter DNA

• Published in: The FEBS journal Vol. 288; no. 15; pp. 4560 - 4575
• Main Authors: Giannopoulou, Evdokia‐Anastasia, Senda, Miki, Koentjoro, Maharani Pertiwi, Adachi, Naruhiko, Ogawa, Naoto, Senda, Toshiya
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.08.2021
• Subjects: Atomic structure; Bends; Binding; Crystal structure; Deoxyribonucleic acid; DNA; DNA complex; DNA structure; Domains; LysR‐type transcriptional regulator; promoter; Protein structure; Proteins; Quaternary structure; transcription; Transcription activation; crystal structure; LysR-type transcriptional regulator; DNA complex; promoter; transcription
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.15764

LysR‐type transcription regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria. They are typically homo‐tetrameric proteins and interact with promoter DNA of ~ 50–60 bp. Earlier biochemical studies have suggested that LTTR binding to promoter DNA bends the DNA and, upon inducer binding, the bend angle of the DNA is reduced through a quaternary structure change of the tetrameric LTTR, leading to the activation of transcription. To date, crystal structures of full‐length LTTRs, DNA‐binding domains (DBD) with their target DNAs, and the regulatory domains with and without inducer molecules have been reported. However, these crystal structures have not provided direct evidence of the quaternary structure changes of LTTRs or of the molecular mechanism underlying these changes. Here, we report the first crystal structure of a full‐length LTTR, CbnR, in complex with its promoter DNA. The crystal structure showed that, in the absence of bound inducer molecules, the four DBDs of the tetrameric CbnR interact with the promoter DNA, bending the DNA by ~ 70°. Structural comparison between the DNA‐free and DNA‐bound forms demonstrates that the quaternary structure change of the tetrameric CbnR required for promoter region‐binding arises from relative orientation changes of the three domains in each subunit. The mechanism of the quaternary structure change caused by inducer binding is also discussed based on the present crystal structure, affinity analysis between CbnR and the promoter DNA, and earlier mutational studies on CbnR. Database Atomic coordinates and structure factors for the full‐length Cupriavidus necator NH9 CbnR in complex with promoter DNA are available in the Protein Data Bank under the accession code 7D98. LysR‐type transcription regulators (LTTRs) comprise one of the largest families of transcriptional regulators in bacteria. To understand the mechanism of the transcription activation by LTTRs, the ternary structure of LTTR in complex with promoter DNA is essential. Here, we report the first crystal structure of a full‐length LTTR, CbnR, in complex with its promoter DNA, and thereby unveil the molecular mechanism of its quaternary structure change.