CRYSTAL-STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT 3.0 ANGSTROM RESOLUTION

The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensu s operator has been determined at 3.0 Angstrom resolution. The structu re confirms the large changes in the protein and DNA seen previously i n a crystallographically distinct low-resolution structure of the comp lex al-td, for the first time, reveals the detailed interactions betwe en the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. lit the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the ''ball and socket'' motif see n in the immunoglobulins and T-cell receptors. The crystal structure o f the Cro complex is consistent with virtually all available biochemic al and related data. Some of the interactions between Cro and DNA prop osed on the basis of model-building are now seen to be correct, but ma ny are different. Tests of the original model by mutagenesis anc-l bio chemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operat or recognition is achieved almost entirely by direct hydrogen-bonding and van der Weals contacts between the protein and the exposed bases w ithin the major groove of the DNA. The discrimination of Cro between t he operators O(R)3 and O(R)1, which differ in sequence at just three p ositions, is inferred to result from a combination of small difference s, both favorable and unfavorable. A van der Waals contact at one of t he positions is of primary importance, while the other two provide sma ller, indirect effects. Direct hydrogen bonding is not utilized in thi s distinction. (C) 1998 Academic Press.