Crystal structure of the DNA‐binding domain of the LysR‐type transcriptional regulator CbnR in complex with a DNA fragment of the recognition‐binding site in the promoter region

• Published in: The FEBS journal Vol. 285; no. 5; pp. 977 - 989
• Main Authors: Koentjoro, Maharani Pertiwi, Adachi, Naruhiko, Senda, Miki, Ogawa, Naoto, Senda, Toshiya
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.03.2018
• Subjects: Alcaligenes; Amino Acid Sequence; Animals; Atomic structure; bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Base Sequence; Binding Sites; CbnR; Crystal structure; Crystallography, X-Ray; Cupriavidus necator; Cupriavidus necator - genetics; Cupriavidus necator - metabolism; Data banks; Deoxyribonucleic acid; DNA; DNA structure; DNA, Bacterial - metabolism; Gene Expression Regulation, Bacterial; LysR‐type transcriptional regulator; Models, Molecular; Nucleotide sequence; Promoter Regions, Genetic; Protein Conformation; Protein Domains; Ralstonia eutropha; Recognition; Regulators; Selectivity; Sequence Alignment; Sequence Homology, Amino Acid; Structure-Activity Relationship; Substrate Specificity; transcription; Transcription activation; Transcription Factors - chemistry; Transcription Factors - metabolism; Transcription, Genetic; X‐ray crystallography; X-ray crystallography; LysR-type transcriptional regulator; bacteria; transcription; CbnR
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.14380

LysR‐type transcriptional regulators (LTTRs) are among the most abundant transcriptional regulators in bacteria. CbnR is an LTTR derived from Cupriavidus necator (formerly Alcaligenes eutrophus or Ralstonia eutropha) NH9 and is involved in transcriptional activation of the cbnABCD genes encoding chlorocatechol degradative enzymes. CbnR interacts with a cbnA promoter region of approximately 60 bp in length that contains the recognition‐binding site (RBS) and activation‐binding site (ABS). Upon inducer binding, CbnR seems to undergo conformational changes, leading to the activation of the transcription. Since the interaction of an LTTR with RBS is considered to be the first step of the transcriptional activation, the CbnR–RBS interaction is responsible for the selectivity of the promoter to be activated. To understand the sequence selectivity of CbnR, we determined the crystal structure of the DNA‐binding domain of CbnR in complex with RBS of the cbnA promoter at 2.55 Å resolution. The crystal structure revealed details of the interactions between the DNA‐binding domain and the promoter DNA. A comparison with the previously reported crystal structure of the DNA‐binding domain of BenM in complex with its cognate RBS showed several differences in the DNA interactions, despite the structural similarity between CbnR and BenM. These differences explain the observed promoter sequence selectivity between CbnR and BenM. Particularly, the difference between Thr33 in CbnR and Ser33 in BenM appears to affect the conformations of neighboring residues, leading to the selective interactions with DNA. Database Atomic coordinates and structure factors for the DNA‐binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP. We solved the crystal structure of the DNA‐binding domain of CbnR, one of the LysR‐type transcription regulators (LTTR), in complex with its recognition DNA element. Despite its structural similarity to another LTTR, BenM, DNA selectivity of CbnR is distinct from that of BenM. The difference between Thr33(CbnR) and Ser33(BenM) accounts for the selective interaction with DNA.