title: Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.
abstract: In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by first forming a complex with the phosphoprotein HPr-Ser46-P. Bacillus subtilis CcpA functions as both a transcription repressor and activator and binds to more than 50 operators called catabolite response elements (cres). These sites are highly degenerate with the consensus, WTGNNARCGNWWWCAW. How CcpA-(HPr-Ser46-P) binds such diverse sequences is unclear. To gain insight into this question, we solved the structures of the CcpA-(HPr-Ser46-P) complex bound to three different operators, the synthetic (syn) cre, ackA2 cre and gntR-down cre. Strikingly, the structures show that the CcpA-bound operators display different bend angles, ranging from 31° to 56°. These differences are accommodated by a flexible linkage between the CcpA helix-turn-helix-loop-helix motif and hinge helices, which allows independent docking of these DNA-binding modules. This flexibility coupled with an abundance of non-polar residues capable of non-specific nucleobase interactions permits CcpA-(HPr-Ser46-P) to bind diverse operators. Indeed, biochemical data show that CcpA-(HPr-Ser46-P) binds the three cre sites with similar affinities. Thus, the data reveal properties that license this protein to function as a global transcription regulator.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. maschuma@mdanderson.org
authors.forename: Maria A
authors.initials: MA
authors.lastname: Schumacher
authors.forename: Mareen
authors.initials: M
authors.lastname: Sprehe
authors.forename: Maike
authors.initials: M
authors.lastname: Bartholomae
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Hillen
authors.forename: Richard G
authors.initials: RG
authors.lastname: Brennan
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry*; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D018360:Crystallography, X-Ray; D004269:DNA, Bacterial / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D009875:Operator Regions, Genetic; D010750:Phosphoproteins / Q000737:chemistry*; D011485:Protein Binding; D020218:Response Elements; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D010750:Phosphoproteins; D014157:Transcription Factors