Chen Y Q, Ghosh S, Ghosh G
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0359, USA.
Nat Struct Biol. 1998 Jan;5(1):67-73. doi: 10.1038/nsb0198-67.
The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.
已确定与DNA靶标结合的NF-κB p65（RelA）同二聚体的晶体结构，分辨率为2.4埃。两个p65亚基在DNA靶标上的排列不对称。同二聚体应最佳地结合到一个假回文九碱基对靶标上，每个亚基识别一个由中央A-T碱基对隔开的5'GGAA-3'半位点。然而，其中一个亚基（亚基B）遇到的半位点是5'-GAAA-3'。从G-C到A-T的单碱基对变化导致该半位点与亚基B中与碱基接触的蛋白质残基之间产生极不利的相互作用，这导致N末端结构域从其正常构象旋转18度。值得注意的是，亚基B与DNA靶标的糖磷酸骨架保留了所有相互作用。这种相互作用模式使NF-κB p65同二聚体能够识别仅包含一个同源半位点的DNA靶标。另一半位点序列的差异提供了复合物构象和亲和力的变化。
