STRUCTURE OF THE ESCHERICHIA-COLI FIS-DNA COMPLEX PROBED BY PROTEIN CONJUGATED WITH 1,10-PHENANTHROLINE COPPER(I) COMPLEX

The Escherichia coil Fis (factor for inversion stimulation) protein fu nctions in many diverse biological systems including recombination, tr anscription, and DNA replication. Although Fis is a site-specific DNA- binding protein, it lacks a well defined consensus recognition sequenc e. The electrophoretic mobility of Fis-DNA complexes, along with consi derations of the Fis crystal structure, indicates that significant def ormation of DNA occurs upon Fis binding. To investigate the structure of Fis-DNA complexes, the chemical nuclease 1,10-phenanthroline-copper complex (OP-Cu) has been linked to four specific sites within the Fis DNA-binding domain. Two of these Fis-OP derivatives were active in cl eaving DNA. The scission patterns obtained on four different Fis bindi ng sites indicate that Fis positions itself on these highly divergent DNA sequences in a very similar fashion. The patterns of cleavage of a derivative at Asn-98 generally support a model of a Fis-DNA complex t hat contains specific bends within the core-recognition sequence. Data from a second Fis-OP derivative at Asn-73 provides evidence for great er wrapping of flanking DNA around the sides of the Fis protein than w as previously postulated. The cleavage efficiency of flanking segments varies, suggesting that the extent of DNA wrapping is sequence depend ent. Specific amino acids on Fis are implicated in promoting this DNA wrapping.