A Bacteriophage Repressor/Operator Complex at 7 Å Resolution
Possible mechanisms for sequence-specific affinity of proteins for DNA include: (1) ‘direct readout’ of base sequence by interactions of residues in the protein with functional groups on the DNA bases; (2) ‘indirect readout’ by interactions with backbone conformations sensitive to base sequence; (3) dependence of binding on long-range structural characteristics of DNA — e.g. twist, bend, or superhelicity; (4) induction of cooperative transitions in DNA, such as B -> A or B -> Z. The crystal structure of a bacteriophage repressor/operator complex, determined at 7 Å resolution, permits us to examine these mechanisms in the context of a particular example (Anderson et al·, 1985). The protein in this complex is the amino-terminal domain (residues 1-69 and denoted Rl-69) of the repressor encoded by coliphage 434, a close relative of bacteriophage λ. The DNA is a 14 base-pair synthetic oligonucleotide, with a self-complementary sequence (Fig. 1) that contains a consensus of the six repressor binding sites (operators) in the phage.
KeywordsBase Sequence Major Groove Backbone Conformation Cooperative Transition Direct Readout
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