Figure 3

Structural details of the four mutations under study. a, ten residues in the spacer IP subdomain that map within 15 Å from K601 are known to have pathogenic human mutations. Yellow coloring shows pathogenic Alpers cluster 2 (DNA binding channel) as defined by Euro et al. [12]. The most common known POLG mutation, A467T, has been reported to have some dominant-like features [16]. b, K601 interacts with A721 (2.3 Å) and E616 (2.6 Å) in the crystal structure of PolGA (PDB:3IKM). The ionic interactions depicted by dashed lines cannot exist with the charge-reversal mutation K601E. c, mutation D122Y lies at the outer periphery of the pol active site access region, within ~25 Å from the active site. Green coloring shows Alpers cluster 1 residues. Cluster 1 contains all of the conserved Pol family A motifs, as well as all known pathogenic mutations in the fingers and palm subdomains of the pol domain. The C-terminus, where mutation Q1236H resides, is considerably further away from the regions that are likely to affect nucleotide polymerization. d, residue Y837 does not form any critical bonds in the PolGA structure. Its surrounding residues assert only limited spatial pressure, and replacement of this residue with a cysteine does not cause obvious effects on the tertiary structure. The nearest mutation studied previously, Y831C, is located six amino acids on the N-terminal side in the primary sequence.