title: pH-dependent conformational switch activates the inhibitor of transcription elongation.
abstract: Gfh1, a transcription factor from Thermus thermophilus, inhibits all catalytic activities of RNA polymerase (RNAP). We characterized the Gfh1 structure, function and possible mechanism of action and regulation. Gfh1 inhibits RNAP by competing with NTPs for coordinating the active site Mg2+ ion. This coordination requires at least two aspartates at the tip of the Gfh1 N-terminal coiled-coil domain (NTD). The overall structure of Gfh1 is similar to that of the Escherichia coli transcript cleavage factor GreA, except for the flipped orientation of the C-terminal domain (CTD). We show that depending on pH, Gfh1-CTD exists in two alternative orientations. At pH above 7, it assumes an inactive 'flipped' orientation seen in the structure, which prevents Gfh1 from binding to RNAP. At lower pH, Gfh1-CTD switches to an active 'Gre-like' orientation, which enables Gfh1 to bind to and inhibit RNAP.
authors.affiliation: Department of Cell Biology, School of Osteopathic Medicine at Stratford, University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084, USA.
authors.forename: Oleg
authors.initials: O
authors.lastname: Laptenko
authors.forename: Seung-Sup
authors.initials: SS
authors.lastname: Kim
authors.forename: Jookyung
authors.initials: J
authors.lastname: Lee
authors.forename: Marina
authors.initials: M
authors.lastname: Starodubtseva
authors.forename: Fellipe
authors.initials: F
authors.lastname: Cava
authors.forename: Jose
authors.initials: J
authors.lastname: Berenguer
authors.forename: Xiang-Peng
authors.initials: XP
authors.lastname: Kong
authors.forename: Sergei
authors.initials: S
authors.lastname: Borukhov
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000037:antagonists & inhibitors / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D016963:Thermus thermophilus / Q000378:metabolism*; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases; D008274:Magnesium