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  • The EMBO Journal (2002) 21, 6257 - 6266
  • doi:10.1093/emboj/cdf627

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

S Singh1, G. E. Folkers1, A. M. J. J. Bonvin1, R Boelens1, R Wechselberger1, A Niztayev1 and R Kaptein1

  1. Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

Correspondence to:

R Kaptein, E-mail: kaptein@nmr.chem.uu.nl

Received 21 January 2002; Accepted 30 September 2002; Revised 25 September 2002

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix–hairpin–helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded–double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop ('bubble DNA'). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine–valine–glycine residues followed by lysine–arginine–arginine, a positively charged surface patch and the second hairpin region consisting of glycine–isoleucine–serine. A model for the protein– DNA complex is proposed that accounts for this specificity.

  • Keywords:

    • bubble DNA,
    • DNA repair,
    • HhH motif,
    • nucleotide excision repair,
    • UvrC C-terminal domain