Figure 4

Analysis of the hydrophobic PIP-box binding pocket on the surface of Hv PCNA. A. Hydrophobic surface of Hv PCNA (left) and uncomplexed Af PCNA (right – [PDB:1RWZ];) with the backbone of the Af Fen1 peptide [PDB:1RXZ];shown in yellow. Amino acids are coloured according to the Kyte-Doolittle scale with blue for the most hydrophilic residues to white (0.0) and orange-red for the most hydrophobic. Produced using Chimera [44]. B. Superposition of Hv PCNA (white) and Af PCNA (beige) [PDB:1RWZ] with the Fen1 peptide depicted in red (from [PDB:1RXZ];. Met46 and Met239 and interdomain connector loop residues are shown in stick representation with atomic colouring (Hv PCNA numbering). C. Alignment of the candidate PIP-boxes of H. volcanii DNA polymerases with the PIP-box consensus sequence and that of Af Fen1 [PDB:1RWZ]. Conserved residues are highlighted in red.