Figure 9.

Comparison of the 3′–5′ exonuclease domain of ExnV1, PolI_G20c and the Klenow fragment.(a) Residues 339–548 of the Klenow fragment (PDB entry 2kzz, orange) are superposed on the corresponding residues of PolI_G20c (PDB entry 7r0k, ice blue) and ExnV1 (PDB entry 7r0t, gold). The SβαR region of ExnV1 and PolI_G20c is marked with a red ring and includes α-helices 7 and 8 and β-strands 8, 9 and 10 of PolI_G20c, which are marked with arrows. (b) Sequence alignment of ExnV1, PolI_G20c and DNA polymerase I from E. coli generated in Jalview with conserved residues (threshold 100%) coloured according to ClustalX. The 3′–5′ exonuclease domain as defined in InterPro is underlined with a red dotted line and the SβαR structural motif is marked with a black box, including α-helices and β-strands of PolI_G20c, which are marked with red and blue lines, respectively, above the alignment. Crucial catalytic residues are marked with red boxes, important residues with secondary roles are marked with orange boxes and Glu357 is marked with a blue box. (c) As (a) but from another angle and with a box indicating an enlarged area containing crucial catalytic residues shown in ball-and-stick representation and important residues with secondary roles, including Glu357, displayed with fat bonds, where residues of the Klenow fragment, PolI_G20c and ExnV1 are coloured brown, blue and dark gold, respectively. (d) An enlarged area of (c). (e) The direct contact between the metal ions and catalytic residues of ExnV1 (numbered according to the corresponding residues of the Klenow fragment). (f) As (c) but with the metal ions and substrate from the model of the Klenow fragment displayed in light blue and the nucleotide and metal ions from ExnV1 displayed in violet.