DNA-binding surface of RecA protein photochemical cross-linking of the first DNA binding site on RecA filament.

The first DNA-binding site (site I) of RecA protein on the filament has been mapped. RecA protein was covalently cross-linked with a 55-base synthetic single-stranded DNA which was a good substrate for the RecA-mediated strand exchange reaction. The cross-linking sites of protein were determined in the regions spanning RecA residues 64-68, 89-106, 178-183, 199-216 and 257-280. The cross-linking in the residues 64-68, 89-106, 199-216 and 257-280 would be due to the cross-linking of Tyr65, Tyr103, disordered loop 2, and Tyr264, respectively. These regions form a DNA-binding surface centered around the beta-sheet spanning residues 243-257. In the P6(1) crystal filament, the DNA-binding surface is near the RecA-RecA interface but are not in the filament axis. The data implicate a mechanism whereby the DNA binding surface would be led into the filament axis by a conformational change from inactive filament as the P6(1) structure to active filament as the RecA-DNA-ATP complex.