Fig. 3: Roles of MtUvrA IDs in DNA clamping and characterization of the damaged-dsDNA binding activity of the wild type enzyme and mutated variants. | Nature Communications

Fig. 3: Roles of MtUvrA IDs in DNA clamping and characterization of the damaged-dsDNA binding activity of the wild type enzyme and mutated variants.

From: Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair

Fig. 3: Roles of MtUvrA IDs in DNA clamping and characterization of the damaged-dsDNA binding activity of the wild type enzyme and mutated variants.

a Closeup of the MtUvrA dimer IDs, showing the structural motifs/elements that are engaged in clamping and deforming the DNA molecule (in orange); in both panels, the region of one DNA strand that is not defined in the model is represented by a dashed line and β-hairpins363-377 were not modeled. b Detailed view of the flipped-out nucleotide; functionally relevant residues of the recognition-ID hydrophobic pocket are displayed as sticks and labeled, as well as Tyr323. c Flipped-out nucleotide in UvrB-DNA complex (PDB: 6O8F)12, accommodating into the hydrophobic pocket between domains 1a and 1b. d SPR sensorgrams of MtUvrA proteins (wild type and mutated variants) binding to the damaged-DNA probe immobilized on a sensor chip. e Calculated Kon, Koff and KD values are shown for each investigated variant. Source data are provided as a Source Data file.

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