Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
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.
Singh
S
S
Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Folkers
G E
GE
Bonvin
A M J J
AM
Boelens
R
R
Wechselberger
R
R
Niztayev
A
A
Kaptein
R
R
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000378:metabolism; D019281:Dimerization; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012996:Solutions; D013329:Structure-Activity Relationship
D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D029968:Escherichia coli Proteins; D012996:Solutions; D004706:Endodeoxyribonucleases; C066567:UvrC protein, E coli