Extended Data Fig. 7: Mutagenesis of the PZL-A binding pocket.
From: Small molecules restore mutant mitochondrial DNA polymerase activity
a, PZL-A in the binding site in the G848S-PZL-A structure, with sidechains from nearby residues displayed as sticks. The protein surface surrounding the compound is coloured by hydrophobicity potential (calculated in UCSF ChimeraX). The binding site is mainly a hydrophobic pocket, with PZL-A wedged between hydrophobic residues from both POLγA (light purple) and POLγB (beige). However, a small hydrophilic patch is located near the polar urea carbonyl group and the chromane oxygen in PZL-A. b, Three residues in POLγA (L566, H569 and W585) are in close proximity to PZL-A and interacts with different parts of the compound. Cryo-EM densities for PZL-A (blue) and the residues (purple) are shown. c, Representative plots of differential scanning fluorimetry performed with POLγA variants in complex with POLγB, in the absence or presence of 10 μM PZL-A. Residues in close proximity to PZL-A (see b) were replaced with alanine (L566A, H569A and W585A). Values are presented as normalized fluorescence (Fnorm) in arbitrary units (A.U.). The difference in melting temperature, ΔTm (mean ± s.d., n = 3 independent experiments) is given. d, Representative plots of differential scanning fluorimetry performed with wild-type POLγA, wild-type POLγB, and the wild-type POLγ complex, in the absence or presence of 10 μM PZL-A. Values are presented as normalized fluorescence (Fnorm) in arbitrary units (A.U.). The difference in melting temperature, ΔTm (mean ± s.d., n = 3 independent experiments) is given. For the wild-type POLγ complex, ΔTm is given for the POLγA subunit.
