Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer in complex with DNA containing an A-tract

The crystal structure of the heterodimer formed by the DNA binding domains of the yeast mating type transcription factors, MATa1 and MAT alpha 2, boun d to a 21 bp DNA fragment has been determined at 2.5 Angstrom resolution. T he DNA fragment in the present study differs at four central base pairs fro m the DNA sequence used in the previously studied ternary complex. These ba se pair changes give rise to a (dA(5)).(dT(5)) tract without changing the o verall base composition of the DNA, The resulting A-tract occurs near the c enter of the overall 60 degrees bend in the DNA, Comparison of the two stru ctures shows that the structural details of the DNA bend are maintained des pite the DNA sequence changes. Analysis of the A(5)-tract DNA subfragment s hows that it contains a bend toward the minor groove centered at one end of the A-tract. The observed bend is larger than that observed in the crystal structures of A-tracts embedded in uncomplexed DNA, which are straight and have been presumed to be quite rigid. Variation of the central DNA base se quence reverses the two AT base pairs contacted in the minor groove by Arg( 7) of the alpha 2 N-terminal arm without significantly altering the DNA bin ding affinity of the a1/alpha 2 heterodimer, The Arg(7) side chain accommod ates the sequence change by forming alternate H bond interactions, in agree ment with the proposal that minor groove base pair recognition is insensiti ve to base pair reversal. Furthermore, the minor groove spine of hydration, which stabilizes the narrowed minor groove caused by DNA bending, is conse rved in both structures, We also find that many of the water-mediated hydro gen bonds between the a1 and alpha 2 homeodomains and the DNA are highly co nserved, indicating an important role for water in stabilization of the a1/ alpha 2-DNA complex.