Helix lap-joints as ion-binding sites: DNA-binding motifs and Ca-binding "EF hands" are related by charge and sequence reversal.
The DNA-binding helix pairs in gene repressor and activator proteins were compared with other approximately perpendicular pairs of adjacent helices in the known protein structures. Two other examples of closely matching conformations were found in cytochrome c peroxidase (residues 153-174) and in ribosomal L7/L12 protein (residues 68-89). Another group of such offset "lap-joints" are the Ca-binding "EF hand" structures, which bind a positive rather than a negative ligand. The EF hands turn out to match the DNA-binding motifs quite well (outside of the loop) if their sequence direction is reversed. This conformation is thus not as unusual as had been thought, but may have a more generalized role in ion binding and occasionally occur in a purely structural role.
Richardson
J S
JS
Department of Biochemistry, Duke University, Durham, North Carolina 27710.
Richardson
D C
DC
D000595:Amino Acid Sequence; D003198:Computer Simulation; D003578:Cytochrome-c Peroxidase; D004268:DNA-Binding Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012097:Repressor Proteins; D012269:Ribosomal Proteins; D013329:Structure-Activity Relationship
D004268:DNA-Binding Proteins; D012097:Repressor Proteins; D012269:Ribosomal Proteins; C016700:ribosomal protein L7-L12; D003578:Cytochrome-c Peroxidase