Loop-to-helix transition in the structure of multidrug regulator AcrR at the entrance of the drug-binding cavity

• Published in: Journal of structural biology 2016-04, Vol.194 (1), p.18-28
• Main Authors: Manjasetty, Babu A., Halavaty, Andrei S., Luan, Chi-Hao, Osipiuk, Jerzy, Mulligan, Rory, Kwon, Keehwan, Anderson, Wayne F., Joachimiak, Andrzej
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; BASIC BIOLOGICAL SCIENCES; Binding Sites; Cloning, Molecular; Crystallography, X-Ray; Hydrogen Bonding; Ligands; Loop-to-helix transition; Models, Molecular; Multidrug resistance; Protein Binding; Protein Domains; Protein Structure, Secondary; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism; Salmonella typhimurium - genetics; Salmonella typhimurium - metabolism; Sequence Homology, Nucleic Acid; TetR/AcrR; Transcription regulator
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2016.01.008

Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56Å resolution. The tertiary and quaternary structures of AcrR are similar to those of its homologs. The multidrug binding site was identified based on structural alignment with homologous proteins and has a di(hydroxyethyl)ether molecule bound. Residues from helices α4 and α7 shape the entry into this binding site. The structure of AcrR reveals that the extended helical conformation of helix α4 is stabilized by the hydrogen bond between Glu67 (helix α4) and Gln130 (helix α7). Based on the structural comparison with the closest homolog structure, the Escherichia coli AcrR, we propose that this hydrogen bond is responsible for control of the loop-to-helix transition within helix α4. This local conformational switch of helix α4 may be a key step in accessing the multidrug binding site and securing ligands at the binding site. Solution small-molecule binding studies suggest that AcrR binds ligands with their core chemical structure resembling the tetracyclic ring of cholesterol.