Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend

• Published in: Journal of molecular biology 2003-05, Vol.328 (3), p.555-566
• Main Authors: Muraoka, Shin, Okumura, Rumi, Ogawa, Naoto, Nonaka, Takamasa, Miyashita, Kiyotaka, Senda, Toshiya
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; cbnR protein; crystal structure; Crystallography, X-Ray; Cupriavidus necator; DNA - chemistry; DNA - metabolism; DNA bending; DNA-binding protein; Escherichia coli Proteins - chemistry; Gene Expression Regulation; Lac Repressors; LysR-type transcriptional regulator; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Promoter Regions, Genetic; Protein Binding; Protein Structure, Quaternary; Protein Structure, Tertiary; Protein Subunits; Ralstonia eutropha; Repressor Proteins - chemistry; Sequence Alignment; Transcription Factors - chemistry; Transcription Factors - metabolism; X-ray crystallography
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(03)00312-7

The LysR-type transcriptional regulator (LTTR) proteins are one of the most common transcriptional regulators in prokaryotes. Here we report the crystal structure of CbnR, which is one of the LTTRs derived from Ralstonia eutropha NH9. This is the first crystal structure of a full-length LTTR. CbnR was found to form a homo-tetramer, which seems to be a biologically active form. Surprisingly, the tetramer can be regarded as a dimer of dimers, whereby each dimer is composed of two subunits in different conformations. In the CbnR tetramer, the DNA-binding domains are located at the V-shaped bottom of the main body of the tetramer, and seem to be suitable to interact with a long stretch of the promoter DNA, which is approximately 60 bp. Interaction between the four DNA-binding domains and the two binding sites on the target DNA is likely to bend the target DNA along the V-shaped bottom of the CbnR tetramer. The relaxation of the bent DNA, which occurs upon inducer binding to CbnR, seems to be associated with a quaternary structure change of the tetramer.