Structural Basis for Converting a General Transcription Factor into an Operon-Specific Virulence Regulator

• Published in: Molecular cell 2007-04, Vol.26 (1), p.117-129
• Main Authors: Belogurov, Georgiy A., Vassylyeva, Marina N., Svetlov, Vladimir, Klyuyev, Sergiy, Grishin, Nick V., Vassylyev, Dmitry G., Artsimovitch, Irina
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; DNA; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - metabolism; Escherichia coli - chemistry; Escherichia coli - enzymology; Escherichia coli - pathogenicity; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Evolution, Molecular; MICROBIO; Molecular Sequence Data; Operon; Peptide Elongation Factors - chemistry; Peptide Elongation Factors - genetics; Peptide Elongation Factors - metabolism; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Structure-Activity Relationship; Trans-Activators - chemistry; Trans-Activators - genetics; Trans-Activators - metabolism; Transcription Factors - chemistry; Transcription Factors, General - chemistry; Transcription, Genetic; Transcriptional Elongation Factors - metabolism; Virulence
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2007.02.021

RfaH, a paralog of the general transcription factor NusG, is recruited to elongating RNA polymerase at specific regulatory sites. The X-ray structure of Escherichia coli RfaH reported here reveals two domains. The N-terminal domain displays high similarity to that of NusG. In contrast, the α-helical coiled-coil C domain, while retaining sequence similarity, is strikingly different from the β barrel of NusG. To our knowledge, such an all-β to all-α transition of the entire domain is the most extreme example of protein fold evolution known to date. Both N domains possess a vast hydrophobic cavity that is buried by the C domain in RfaH but is exposed in NusG. We propose that this cavity constitutes the RNA polymerase-binding site, which becomes unmasked in RfaH only upon sequence-specific binding to the nontemplate DNA strand that triggers domain dissociation. Finally, we argue that RfaH binds to the β′ subunit coiled coil, the major target site for the initiation σ factors.