THE X-RAY STRUCTURE OF THE PURR-GUANINE-PURF OPERATOR COMPLEX REVEALSTHE CONTRIBUTIONS OF COMPLEMENTARY ELECTROSTATIC SURFACES AND A WATER-MEDIATED HYDROGEN-BOND TO COREPRESSOR SPECIFICITY AND BINDING-AFFINITY

The purine repressor, PurR, is the master regulatory protein of de nov o purine nucleotide biosynthesis in Escherichia coli. This dimeric tra nscription factor is activated to bind to cognate DNA operator sites b y initially binding either of its physiologically relevant, high affin ity corepressors, hypoxanthine (K-d = 9.3 mu M) or guanine (K-d = 1.5 mu M). Here, we report the 2.5-Angstrom crystal structure of the PurR- guanine-purF operator ternary complex and complete the atomic descript ion of 6-oxopurine-induced repression by PurR. As anticipated, the str ucture of the PurR-guanine-purF operator complex is isomorphous to the PurR-hypoxanthine-purF operator complex, and their protein-DNA and pr otein-corepressor interactions are nearly identical. The former findin g confirms the use of an identical allosteric DNA-binding mechanism wh ereby corepressor binding 40 Angstrom from the DNA-binding domain juxt aposes the hinge regions of each monomer, thus favoring the formation and insertion of the critical minor groove-binding hinge helices. Stri kingly, the higher binding affinity of guanine for PurR and the abilit y of PurR to discriminate against 2-oxopurines do not result from dire ct protein-ligand interactions, but rather from a water-mediated conta ct with the exocyclic N-2 of guanine, which dictates the presence of a donor group on the corepressor, and the better electrostatic compleme ntarity of the guanine base and the corepressor-binding pocket.