title: P22 c2 repressor-operator complex: mechanisms of direct and indirect readout.
abstract: The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps to direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. We describe the 1.6 A X-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2. This operator has an A-T base pair at position 9L and a T-A base pair at position 9R and is termed DNA9T. Direct readout: nondirectional van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD-DNA9T complex suggests that sequence-specificity arises substantially from lock-and-key interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5'-TTAA-3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational changes. Protein-DNA hydrogen bonding plays a secondary role in specificity. Indirect readout: it is known that the noncontacted bases in the center of the complex are important determinants of affinity. The protein induces a transition of the noncontacted region from B-DNA to B'-DNA. The B' state is characterized by a narrow minor groove and a zigzag spine of hydration. The free energy of the transition from B- to B'-DNA is known to depend on the sequence. Thus, the observed DNA conformation and hydration allows for the formulation of a predictive model of the indirect readout phenomenon.
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
authors.forename: Derrick
authors.initials: D
authors.lastname: Watkins
authors.forename: Chiaolong
authors.initials: C
authors.lastname: Hsiao
authors.forename: Kristen Kruger
authors.initials: KK
authors.lastname: Woods
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Koudelka
authors.forename: Loren Dean
authors.initials: LD
authors.lastname: Williams
mesh_terms: D020029:Base Pairing / Q000502:physiology; D001483:Base Sequence; D001665:Binding Sites; D015374:Biosensing Techniques / Q000379:methods; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity; D014867:Water / Q000494:pharmacology
chemical_list: D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D014867:Water; D004247:DNA