Mechanism of DNA binding to the gene 5 protein of bacteriophage fd.

A model for the bimolecular complex arising from the interaction of single-stranded DNA with the gene 5 DNA binding protein (G5BP) of bacteriophage fd is proposed on the basis of difference Fourier analyses and the correlation between structural and physicochemical data. The essential DNA binding element is the G5BP dimer which provides two antiparallel DNA binding channels, each constructed from amino acid contributions of both monomers within the pair. These channels display identical bonding environments but opposite polarities as a consequence of the inherent dyad symmetry within each dimer unit. The two channels are separated by 30 A, and each is 10 A wide and 40 A long. We propose that DNA binding is a consequence of two general sets of interactions. Aromatic side chains of G5BP stack upon nucleic acid bases, and the DNA phosphate backbone is bound by a series of appropriately positioned lysyl and arginyl side chains. The DNA conformation is fully extended, and each binding channel can accommodate up to five nucleotides. Only minor conformational changes in the native G5BP structure are required to optimize the binding of DNA. The G5BP-DNA complexation model presented here serves to explain some of the mechanistic features associated with the role this protein plays in the formation of a nucleoprotein helix during the bacteriophage fd life cycle.