A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix

• Published in: Nucleic acids research 2010-08, Vol.38 (15), p.5226-5241
• Main Authors: León, Esther, Navarro-Avilés, Gloria, Santiveri, Clara M, Flores-Flores, Cesar, Rico, Manuel, González, Carlos, Murillo, Francisco J, Elías-Arnanz, Montserrat, Jiménez, María Angeles, Padmanabhan, S
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Binding Sites; DNA; DNA - chemistry; DNA-Binding Proteins - chemistry; Hydrophobicity; Models, Molecular; Molecular Sequence Data; Mutagenesis, Site-Directed; Myxococcus xanthus; N.M.R; Nuclear Magnetic Resonance, Biomolecular; Operator Regions, Genetic; Operators; Operons; Phages; Prokaryotes; Promoters; Protein interaction; Protein Structure, Secondary; Repressor Proteins - chemistry; Repressors; src Homology Domains; Structural Biology; Structure-function relationships; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription initiation
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq277

Direct targeting of critical DNA-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. Structural descriptions for this, though often proposed for bacterial and phage repressor-antirepressor systems, are unavailable. Here, we describe the structural and functional basis of how the Myxococcus xanthus CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarA and CarH repress the carB operon in the dark. CarS, produced in the light, physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB. The NMR structure of CarS1, a functional CarS variant, reveals a five-stranded, antiparallel beta-sheet fold resembling SH3 domains, protein-protein interaction modules prevalent in eukaryotes but rare in prokaryotes. NMR studies and analysis of site-directed mutants in vivo and in vitro unveil a solvent-exposed hydrophobic pocket lined by acidic residues in CarS, where the CarA DNA recognition helix docks with high affinity in an atypical ligand-recognition mode for SH3 domains. Our findings uncover an unprecedented use of the SH3 domain-like fold for protein-protein recognition whereby an antirepressor mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription.