Structural Studies of Three DNA Binding Proteins: Catabolite Gene Activator Protein, Resolvase, and the Klenow Fragment of DNA Polymerase I

Abstract

We have been studying the crystal structure of three proteins that interact with DNA: the E. coli catabolite gene activator protein (CAP) whose structure was determined at 2.9 A resolution (1,2) and is now refined to 2.5 A resolution (3), the Klenow fragment of E. coli DNA polymerase whose structure has been determined from a 3.3 A resolution electron density map (4) and gamma-delta resolvase, a site-specific recombination protein whose structure determination is still in progress (5,6,7). In addition to working out the mechanism by which each of these proteins carries out its biological function, we have been interested in ascertaining the ways in which these proteins are similar or differ in their manner of interaction with double-stranded DNA. Both CAP and resolvase contain small DNA binding domains which confer their DNA sequence specificity (1,6). In both cases the principles of DNA sequence specific interaction appear to be very similar: side-chains from protruding alpha-helices penetrate the DNA major groove and interact with the exposed edges of base pairs. DNA polymerase, on the other hand, contains a very large cleft which is able to nearly surround a double-stranded DNA substrate.