THE COMPLEX BETWEEN PHAGE-434 REPRESSOR DNA-BINDING DOMAIN AND OPERATOR SITE O(R)3 - STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NONCONSENSUS HALF-SITES
Dw. Rodgers et Sc. Harrison, THE COMPLEX BETWEEN PHAGE-434 REPRESSOR DNA-BINDING DOMAIN AND OPERATOR SITE O(R)3 - STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NONCONSENSUS HALF-SITES, Structure, 1(4), 1993, pp. 227-240
Background: The repressor of phage 434 binds to a set of operator site
s as a homodimer. Its relative affinities for these sites determine th
e switch from lysogenic to lytic growth. The six 434 operator sites (O
(R)1, O(R)2, O(R)3, O(L)1, O(L)2 and O(L)3) have a particularly simple
organization; all are 14 base pairs long, with a conserved 5'-ACAA se
quence symmetrically placed at either end, and a variable central six
base pairs. O(R)3 is unique among naturally-occurring 434 operator sit
es in that it contains a non-consensus base pair, G.C, at the fourth p
osition of the otherwise invariant 5'-ACAA sequence. Comparisons among
structures of the 434 repressor DNA-binding domain, R1-69, bound to v
arious operator sites, allow us to analyze differential specificity in
regulatory complexes of this kind. Results: We have determined the st
ructure at 2.5 Angstrom resolution of a complex of R1-69 with DNA cont
aining the O(R)3 Site and compared it with previously studied complexe
s of R1-69 bound to O(R)1 and O(R)2. There are surprisingly extensive
structural differences between the consensus and non-consensus half-si
tes of O(R)3 with respect to their interactions with R1-69, including
a shift in the DNA backbone and a small rotation of the entire R1-69 m
onomer. Conclusions: Recognition of the base pair difference that is c
ritical for the 434 regulatory switch involves a number of amino acid
residues, not just the one or two side chains in direct contact with t
he G.C base pair. Moreover, the repressor imposes a somewhat altered D
NA conformation on the non-consensus half-site.