Figure 8.

(A) Ribbon representation of the structural model of GA-1 DNA polymerase. Models for both GA-1 and Nf DNA polymerases were provided by the homology-modelling server Swiss-Model, using as template the crystallographic structure of φ29 DNA polymerase (PDB code 1XHX). The 3′–5′ exonuclease domain is shown in red, the palm in pink, the fingers in dark blue and the thumb in green. Protein-primed DNA polymerases specific insertions TPR1 and TPR2 are coloured in orange and cyan, respectively. Alignment of the amino acid sequences corresponding to family B motifs of the related φ29, GA-1 and Nf DNA polymerases are shown, as well as their spatial placement. Catalytic amino acids responsible for the exonuclease and the polymerization activities are coloured in red, DNA ligand residues in blue, those interacting with both DNA and TP substrates are in orange, incoming nucleotide ligands in magenta, and residues predicted to make contacts with TP-DNA in green. The linear arrangement of these sequence motifs is shown at the bottom. (B) Structural differences in the TPR1 loop of GA-1 and φ29 DNA polymerases. Superposition of the modelled GA-1 DNA polymerase and crystal structure of φ29 DNA polymerase was obtained by fitting the catalytic amino acid residues responsible of both the exonuclease and polymerization activities by using the Swiss-PdbViewer program (http://www.expasy.org/spdbv/) and further rendering with Pymol (http://www.pymol.org). Figure is restricted to the TPR1 loop region of both DNA polymerases. The DNA has been taken from the structure of the RB69 ternary complex (50) and homology modeled by aligning the palm subdomains of RB69, GA-1 and φ29 DNA polymerases. φ29 and GA-1 DNA polymerases are coloured in cyan and green, respectively. The alignment of the β-turn-β structure of TPR1 insertion is shown at the bottom. Arg and Phe residues located at the tip of the TPR1 loop are shown in orange and yellow, respectively.