“Acceptor–Donor–Acceptor” Motifs Recognize the Watson–Crick, Hoogsteen and Sugar “Donor–Acceptor–Donor” Edges of Adenine and Adenosine-containing Ligands

Abstract

Nucleotides are among the most extensively exploited chemical moieties in nature and, as a part of a handful of different protein ligands, nucleotides play key roles in energy transduction, enzymatic catalysis and regulation of protein function. We have previously reported that in many proteins with different folds and functions a distinctive adenine-binding motif is involved in the recognition of the Watson–Crick edge of adenine. Here, we show that many proteins do have clear structural motifs that recognize adenosine (and some other nucleotides and nucleotide analogs) not only through the Watson–Crick edge, but also through the sugar and Hoogsteen edges. Each of the three edges of adenosine has a donor–acceptor–donor (DAD) pattern that is often recognized by proteins via a complementary acceptor–donor–acceptor (ADA) motif, whereby three distinct hydrogen bonds are formed: two conventional N–H⋯O and N–H⋯N hydrogen bonds, and one weak C–H⋯O hydrogen bond. The local conformation of the adenine-binding loop is βββ or ββα and reflects the mode of nucleotide binding. Additionally, we report 21 proteins from five different folds that simultaneously recognize both the sugar edge and the Watson–Crick edge of adenine. In these proteins a unique β-loop-β supersecondary structure grasps an adenine-containing ligand between two identical adenine-binding motifs as part of the βαβ-loop-β fold.