Figure 2
Alignment of the new Mg2+-bound APE1 structure with DNA-bound structures. (a) Recently determined structure of the APE1 enzyme-product (EP) complex (green; PDB entry 4iem ; Tsutakawa et al., 2013BB53) aligned with the structure of Mg2+-bound APE1 (cyan) reported here. DNA from the EP complex (orange) contains a 3'-OH and a 5'-deoxyribose phosphate (dRP). The Mg2+ ion from the EP complex is colored green and its coordination is indicated by black dotted lines. The Mg2+ ion from the new DNA-free structure is colored cyan and its coordination is indicated by cyan dotted lines, with coordinating water molecules shown as red stars. Hydrogen-bond interactions (yellow dashes) are shown for the EP complex only. The approximate locations of the A and B sites are noted (gray symbols). (b) Structure of the APE1 enzyme-substrate (ES) complex (green; PDB entry 1dew ; Mol et al., 2000BB41) aligned with the new structure of Mg2+-bound APE1 (cyan). The DNA in the ES complex (orange) contains an intact abasic site and Mg2+ was omitted from the ES complex to halt P-O bond cleavage. The green sphere indicates the position of the Mg2+ ion in the EP complex (also aligned with DNA-free APE1). Mg2+ in the DNA-free structure is shown in cyan; its coordination is indicated by cyan dotted lines, with coordinating waters shown as red stars. Hydrogen-bond interactions (yellow dashes) are shown for the ES complex. The potential nucleophilic water from our DNA-free structure is shown as a red star, with cyan dashes indicating hydrogen bonds to Asp210 and Asn212. This water molecule was also observed in previous structures of APE1 with Sm3+ or a single Pb2+ ion (Fig. 1[link]). The approximate locations of the A and B sites are noted (gray symbols).  [article HTML]