φ29 DNA polymerase residue Lys529.

(A) Crystallographic data corresponding to φ29 DNA polymerase binary complex are from Protein Data Bank (PDB) ID 2PZS [13]. A detailed picture shows residue Lys529 (represented as spheres), placed at the C-terminus of the palm subdomain, interacting with the phosphates of the last phosphodiester bond. Primer and template strands are depicted as yellow and cyan sticks, respectively. The 3′ terminal nucleotide of the primer strand, placed at the priming site of the polymerase, is colored in magenta. (B) Amino acid sequence alignment of the C-terminal region of the palm subdomain and TP-priming loop of protein-primed DNA polymerases and TPs, respectively. DNA polymerases accession numbers are as follow: φ29 DNA polymerase (GenBank accession number CAA37450.1), PRD1 DNA polymerase (NCBI reference sequence NP040682.1), Nf DNA polymerase (GenBank accession number ACH57069.1), GA-1 DNA polymerase (GenBank accession number CAA65712.1) and Cp-1 DNA polymerase (GenBank accession number Q37989). Numbers indicate the position of the first aligned amino acid with respect to the N-terminus of the corresponding DNA polymerase. The conserved Lys residue is written in bold letter. TPs accession numbers are as follow: φ29 (UniProtKB accession number P03681), GA-1 (NCBI Reference sequence NP073686.1), Nf (GenBank accession number ACH57070.1), PRD1 (GenBank AAA32449.1) and Cp-1 (NCBI Reference Sequence NP044816.1). Numbers indicate the position of the first aligned amino acid with respect to the N-terminus of the respective TP. The conserved Glu/Asp residue is written in bold letter. The priming residue is indicated with an arrow.