Structural Basis for DNA-Hairpin Promoter Recognition by the Bacteriophage N4 Virion RNA Polymerase

Coliphage N4 virion-encapsidated RNA polymerase (vRNAP) is a member of the phage T7-like single-subunit RNA polymerase (RNAP) family. Its central domain (mini-vRNAP) contains all RNAP functions of the full-length vRNAP, which recognizes a 5 to 7 base pair stem and 3 nucleotide loop hairpin DNA promoter. Here? we report the X-ray crystal structures of mini-vRNAP bound to promoters. Mink vRNAP uses four structural motifs to recognize DNA sequences at the hair in loop and stem and to unwind DNA, Despite their low sequence similarity, three put of four motifs are shared with, T7 RNAP that recognizes a double-stranded DNA promoter. The binary complex structure and results of engineered disulfide linkage experiments reveal that the plug and motif B loop, which block the access of template DNA to the active site in the apo-form mini-vRNAP, undergo a large-scale conformational change upon in promoter binding, explaining the restricted promoter specificity that is critical for N4 phage early transcription.