DNA Synthesis across an Abasic Lesion by Human DNA Polymerase ι Deepak T. Nair, Robert E. Johnson, Louise Prakash, Satya Prakash, Aneel K. Aggarwal  Structure  Volume 17, Issue 4, Pages 530-537 (April 2009) DOI: 10.1016/j.str.2009.02.015 Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 1 PolιAbasic.dNTP Ternary Complexes and Corresponding Simulated Annealed Omit Maps of the Incipient “Base Pairs” (A) PolιAbasic.dGTP ternary complex (left), shown for one of the two Polι molecules bound to a double-ended template primer. The palm, fingers, and thumb domains and the PAD in the Polι molecule are shown in cyan, yellow, orange, and green, respectively. DNA is shown in gray, abasic lesion and incoming dGTP are in red, and the putative Mg2+ ions are displayed as dark blue spheres. The simulated annealing Fo − Fc omit map (contoured at 3.0σ) for the abasic lesion and incoming dGTP is shown on the right. (B) PolιAbasic.dTTP ternary complex and corresponding simulated annealing Fo − Fc omit map. (C) PolιAbasic.dATP ternary complex and corresponding simulated annealing Fo − Fc omit map. Structure 2009 17, 530-537DOI: (10.1016/j.str.2009.02.015) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 2 Active Sites (A) Close-up view of the PolιAbasic.dGTP ternary complex active site region. The coloring scheme is the same as in Figure 1. Highlighted and labeled are the catalytic residues (D34, D126, and E127) and some of the residues apposed close to the abasic lesion (Q59, K60, Y61, L62, S307, and R347) and incoming dNTP (Y39, V64, T65, K77, L78, Y68, R71, and K214). The water molecules that participate in forming water-mediated interactions are displayed as magenta spheres. (B) Close-up view of the PolιAbasic.dTTP ternary complex active site region. The putative Mg2+ ions (A and B) are shown as dark blue spheres. (C) Close-up view of the PolιAbasic.dATP ternary complex active site region. Structure 2009 17, 530-537DOI: (10.1016/j.str.2009.02.015) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 3 Hydrogen-Bonding Networks (A) Hydrogen bonding between the dGTP base and polymerase in the PolιAbasic.dGTP ternary complex. The relevant DNA and protein residues are colored according to element, the water molecules are shown as red spheres, and the hydrogen bonds are displayed as dashed lines. (B) Hydrogen bonding between the dTTP base and polymerase in the PolιAbasic.dTTP ternary complex. (C) Hydrogen bonding between the dATP base and polymerase in the PolιAbasic.dATP ternary complex. Structure 2009 17, 530-537DOI: (10.1016/j.str.2009.02.015) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 4 Comparison of Dpo4Abasic.dCTP and PolιAbasic.dTTP Ternary Complexes The protein surface is displayed in light blue (Dpo4) or cyan (Polι), DNA is shown in stick representation, and putative Mg2+ (Polι) or Ca2+ (Dpo4) ions are shown as dark blue spheres. The abasic site and the incoming dTTP (Polι) or dCTP (Dpo4) are colored in red. The nucleotide 5′ to the abasic site in the Dpo4 complex is colored in sky blue. The abasic site is extrahelical in the Dpo4 complex (Ling et al., 2004), but remains intrahelical in the Polι complex(es). Structure 2009 17, 530-537DOI: (10.1016/j.str.2009.02.015) Copyright © 2009 Elsevier Ltd Terms and Conditions