The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.
BACKGROUND
The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind.


RESULTS
We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer.


CONCLUSIONS
Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.
Rodgers
D W
DW
Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138.
Harrison
S C
SC
D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D018360:Crystallography, X-Ray / Q000379:methods; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D012097:Repressor Proteins / Q000737:chemistry*
D004268:DNA-Binding Proteins; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins