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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 Å 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 DNA^9T. Direct readout:  nondirectional van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD−DNA^9T 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 DNA^9T. The cleft is formed by four methyl groups on sequential base pairs of 5‘-TTAA-3‘. The valine cleft is …