DNA recognition by β-sheets

Abstract

The modes of DNA recognition by β‐sheets are analyzed by using the known crystal and solution three‐dimensional structures of DNA‐protein complexes. Close fitting of the protein surface and the DNA surface determines the binding geometry. Interaction takes place so that essentially the N‐to‐C direction of the β‐strands either follows or crosses the DNA groove. Upon following the major groove a two‐stranded antiparallel β‐sheet dives into the groove and contacts DNA bases with its convex side facing the DNA, while upon following the minor groove, it binds around the sugar‐phosphate backbones, with its opposite concave side shielding the DNA. In order for the β‐strands crossing the minor groove to interact with the DNA, the dinucleotide steps need to almost totally helically untwist and roll around major groove. The β‐sheet, on the other hand, needs to adopt a concave curvature on the binding surface in the direction that follows the DNA minor groove, and a convex surface in the direction that bridges the sugar‐phosphate backbones across the groove. The result is to produce a hyperbolic paraboloidal DNA‐binding surface. © 1998 John Wiley & Sons, Inc. Biopoly 44: 335–359, 1997

Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition

“…A number of other DNA‐binding domains use β‐strands to recognize their target sites in the major groove of the DNA (Tateno et al ., 1997). In proteins of the MetJ/Arc family (Somers and Phillips, 1992; Raumann et al ., 1994) and in the plasmid‐encoded transcriptional repressor CopG (Gomis‐Ruth et al ., 1998), a two‐stranded antiparallel β‐sheet inserts into the major groove with the plane of the two‐stranded sheet reposing on the edges of the bases (Figure 7).…”

Protein – DNA interactions: the story so far and a new method for prediction

“…Much of this has involved the description of specific complexes (for review of recently solved structures, see1) and of families of proteins sharing the same DNA binding motif (e.g. 6, 2, 19).…”

Specificity of hydroxylmethyluracil-containing DNA for transcription factor 1: Structural insights

“…Transcription factor 1 is a phage‐encoded type II DNA‐binding protein that preferentially binds to hmU‐DNA. The β‐ribbon DNA binding motif of type II DNA‐binding proteins were reviewed recently 38, 39. Members of the DBPII family adopt similar tertiary and quarternary structures 20, 22, 40.…”