Fig. 5

PolD-PCNA interaction. a Side view of Form A. The C-terminal loop of DP2, making a contact via PIP-box motif with PCNA is indicated by the black arrow. The “PIP-loop” and the “DP1-loop” are shown in yellow surface. The “switch hook” to contact with DP1 and DP2, respectively, are indicated by the red arrow and red broken arrow, respectively. The switch hook E171 is shown in red and orange sphere representation. b Another view of Form A, rotated by 45° around the vertical axis. The R781 of DP2 making a contact with E171 of PCNA, is shown by blue sphere representation. The E171 of two PCNA subunits used for DP1-PCNA contact are highlighted by red and orange sphere representation, c A closer view of DP1-PCNA contact in a and b. The loop density corresponding to K321-I338 (DP1-loop) is colored yellow. d Conservation of the PolD-PCNA contact sites, DP1-K326, DP2-R434, and DP2-R781. The homologous sequences of DP1 (34 Thermococcus, 14 Candidatus, 9 Pyrococcus, 5 Thermococci, and 24 other species) and DP2 (35 Thermococcus, 10 Pyrococcus, 9 Methanolobus, 6 Thermococci, and 41 other species) were aligned and applied to WebLogo [36]. e Side view of Form B. The C-terminal loop of DP2 making a contact via PIP-box motif with PCNA is indicated by the black arrow. The E171 used in DP1-PCNA interaction of Form A is shown in red sphere representation. A novel contact distinct from that of Form A was indicated by the magenta arrow. The third switch hook E171 is shown in magenta sphere representation. R434 of the DP2 central domain (blue sphere) is assumed to interact with the E171 residue. f A closer view of DP2-PCNA contact shown in e. The positions of the side chains are those of crystal structures and should be regarded as approximate ones