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Volume 21, Issue 2, Pages 247-256 (February 2013) Structural Characterization of a Mouse Ortholog of Human NEIL3 with a Marked Preference for Single-Stranded DNA  Minmin Liu, Kayo Imamura, April M. Averill, Susan S. Wallace, Sylvie Doublié  Structure  Volume 21, Issue 2, Pages 247-256 (February 2013) DOI: 10.1016/j.str.2012.12.008 Copyright © 2013 Elsevier Ltd Terms and Conditions

Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 1 MmuNeil3Δ324 Preferentially Binds to ssDNA (A) Representative gel from the EMSA of MmuNeil3Δ324 E3Q binding to 30-mer single-stranded (left) or duplex (right) substrates containing spiroiminodihydantoin (Sp1). Enzyme and substrate concentrations are as listed. (B) Quantification of the EMSA of MmuNeil3Δ324 E3Q bound to 30-mer single-stranded (left) or duplex (right) substrates containing Sp1. The fraction of the bound substrates was plotted relative to enzyme concentration. Data for single-stranded Sp1 were fit with a single hyperbola to calculate KDapp values. The error bars represent the standard deviation from three independent experiments. Also see Figure S5. Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 2 Overall Structure of MmuNeil3Δ324 (A) Ribbon diagram of MmuNeil3Δ324. The secondary structure elements were defined by DSSP (Kabsch and Sander, 1983) and are: αA (3–16), β1 (23–27), β2 (73–79), β3 (82–87), β4 (90–96), β5 (101–104), β6 (119–123), β7 (127–131), β8 (133–139), αB (140–150), αC (162–171), αD (177–182), αE (192–202), αF (215–238), β9 (262–264), and β10 (273–275). Helices are shown in green and β strands in pink. Residues 37–59 and 113–116 are disordered and are represented by green dots. The zinc metal ion is shown as a gray sphere. (B) Superposition of αB-αC from MmuNeil3Δ324 (green, residues 141–172) to the corresponding segments from the Fpg proteins: Escherichia coli Fpg (EcoFpg, red: PDB ID code 1K82 [Gilboa et al., 2002], residues 118–147), Thermus thermophilus Fpg (TthFpg, pink: PDB ID code 1EE8 [Sugahara et al., 2000], residues 109–140), Lactococcus lactis Fpg (LlaFpg, blue: PDB ID code 1TDZ [Coste et al., 2004], residues 119–150), and Bacillus stearothermophilus Fpg (BstFpg, gold: PDB ID code 1R2Y [Fromme and Verdine, 2003a], residues 122–153). (C) Superposition of αB-αC from MmuNeil3Δ324 (green) to the corresponding segments from the Nei proteins: Escherichia coli Nei (EcoNei, cyan: PDB ID code 1K3W [Zharkov et al., 2002], residues 113–145), NEIL1 (blue: PDB ID code 1TDH [Doublié et al., 2004], residues 126–151), and Mimivirus Nei1 (MvNei1, red: PDB ID code 3A46 [Imamura et al., 2009], residues 122–153). (D) Close-up view of the interdomain hinge. Interacting residues are shown as stick models. Hydrogen bonds and salt bridges are represented by black dashed lines. Also see Figure S1. Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 3 The DNA Binding Cleft and Lesion-Binding Pocket of MmuNeil3Δ324 (A) Electrostatic surface representation of MmuNeil3Δ324 calculated by the program GRASP (Nicholls et al., 1991), colored according to the electrostatic potential (blue, positive; red, negative). DNA from the MvNei1-Tg complex (PDB code: 3VK8; [Imamura et al., 2012]) was superimposed onto MmuNeil3Δ324. The Tg-containing strand is in orange and the complementary strand is in green. (B) Superposition of MmuNeil3 (green) and MvNei1 in complex with Tg-containing DNA (PDB code: 3VK8 [Imamura et al., 2012]; pink) with Tg shown in gold. Hydrogen bonds between MvNei1 and Tg are represented by black dashed lines. Also see Figure S2. Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 4 The Void-Filling Residues of Fpg Contribute to Binding to dsDNA (A) Superposition of the β4-β5 and β7-β8 loops from MmuNeil3 (green) and BstFpg (gold, PDB ID code: 1R2Y [Fromme and Verdine, 2003a]). The β7-β8 loop in MmuNeil3 is shorter and lacks two of the void-filling residues. (B) Analysis of the EMSA of the EcoFpg β7-β8 loop variant binding to duplex DNA containing THF (blue), 8-oxoG (red), or a normal base G (green). (C) Analysis of the EMSA of wild-type EcoFpg binding to duplex DNA containing THF (blue), 8-oxoG (red), or a normal base G (green). The fraction of the bound substrates was plotted relative to enzyme concentration. Data for wild-type EcoFpg were fit with a single hyperbola to calculate KDapp values. The KDapp values of wild-type EcoFpg for THF:C and 8-oxoG:C are 4.5 ± 0.5 nM and 3.7 ± 0.6 nM, respectively. The error bars represent the standard deviation from three independent experiments. Also see Figure S4. Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 5 Close-Up View of the αF-β9 Loop of Fpg/Nei Enzymes (A) Superposition of the αF-β9 loop from MmuNeil3Δ324 (green, residues 224–248) with BstFpg (gold, PDB ID code: 1R2Y [Fromme and Verdine, 2003a], residues 206–240) and TthFpg (pink, PDB ID code: 1EE8 [Sugahara et al., 2000], residues 193–229). (B) with EcoNei (cyan, PDB ID code: 1Q39 [Golan et al., 2005], residues 200–228) and NEIL1 (blue, PDB ID code: 1TDH [Doublié et al., 2004], residues 228–261). The flipped-out 8-oxoG from the BstFpg-DNA complex (PDB ID code: 1R2Y [Fromme and Verdine, 2003a] is shown in orange. Also see Figure S3. Structure 2013 21, 247-256DOI: (10.1016/j.str.2012.12.008) Copyright © 2013 Elsevier Ltd Terms and Conditions