Structural basis for the DNA-binding activity of the bacterial β-propeller protein YncE

beta-Propellers are widely utilized in nature as recognition modules. The well conserved beta-propeller fold exhibits a high degree of functional diversity, which is probably accomplished through variations in the surface properties of the proteins. Little is known about the interactions between beta-propeller proteins and nucleic acids. In the present study, it has been found that the bacterial beta-propeller protein YncE binds to DNA. Crystal structures of YncE in the free form and complexed with DNA revealed that the surface region of YncE corresponding to the 'canonical' substrate-binding site forms essential contacts with DNA. A single DNA base within a single-stranded DNA region is trapped in the hydrophobic pocket located within the central channel of the beta-propeller protein. These data provide physical evidence for the DNA-binding ability of the previously uncharacterized YncE and also suggest that the 'canonical' substrate-binding site may be commonly adapted to facilitate nucleic acid binding in a subset of beta-propeller proteins.