Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2021-11, Vol.77 (11), p.1411-1424
• Main Authors: Šoltysová, Markéta, Sieglová, Irena, Fábry, Milan, Brynda, Jiří, Škerlová, Jana, Řezáčová, Pavlína
• Format: Article
• Language: English
• Subjects: Bacillus subtilis; Bacillus subtilis - chemistry; Bacillus subtilis - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; carbohydrate catabolism; Carbohydrate metabolism; Carbohydrates; Crystal structure; Crystallography, X-Ray; Deoxyribonucleic acid; deoxyribonucleoside regulator bsDeoR; Dimers; DNA; DNA - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Domains; gene regulator bsCggR; Glycolysis; Grooves; Homeobox; Models, Molecular; Nucleotide sequence; Operators; Protein Binding; Protein Conformation; Proteins; protein–DNA complexes; Quorum sensing; Recognition; SorC/DeoR family; Subgroups; Transcription; transcription repressors
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798321009633

The SorC/DeoR family is a large family of bacterial transcription regulators that are involved in the control of carbohydrate metabolism and quorum sensing. To understand the structural basis of DNA recognition, structural studies of two functionally characterized SorC/DeoR family members from Bacillus subtilis were performed: the deoxyribonucleoside regulator bsDeoR and the central glycolytic genes regulator bsCggR. Each selected protein represents one of the subgroups that are recognized within the family. Crystal structures were determined of the N‐terminal DNA‐binding domains of bsDeoR and bsCggR in complex with DNA duplexes representing the minimal operator sequence at resolutions of 2.3 and 2.1 Å, respectively. While bsDeoRDBD contains a homeodomain‐like HTH‐type domain, bsCggRDBD contains a winged helix–turn–helix‐type motif. Both proteins form C2‐symmetric dimers that recognize two consecutive major grooves, and the protein–DNA interactions have been analyzed in detail. The crystal structures were used to model the interactions of the proteins with the full DNA operators, and a common mode of DNA recognition is proposed that is most likely to be shared by other members of the SorC/DeoR family. The first structural insight is provided into DNA recognition by the SorC/DeoR family of bacterial transcriptional regulators. Crystal structures of the DNA‐binding domains of CggR and DeoR from Bacillus subtilis were determined in complexes with their DNA operators.