The Fpg/Nei Family of DNA Glycosylases: Substrates, Structures, and Search for Damage - Progress in Molecular Biology - page 77

A

Zn

Pro2

C-terminal
domain

N-terminal
domain

B

Zn

Pro2

N-terminal
domain

C-terminal
domain

F IG . 1. Overall structural comparison between EcoFpg and EcoNei. (A). EcoFpg bound to
DNA. Both N- and C-terminal domains are colored in purple (PDB ID 1K82). 55 (B) EcoNei bound
to DNA. N- and C-terminal domains are shown in pale pink (IK3W from the PDB). 56 Zinc atoms
are shown as gray spheres in both cases and the DNA is displayed as a ribbon. PyMol was used to
generate the figures (DeLano Scientific, The PyMOL Molecular Graphics System, Version
1.2r3pre, Schr ¨ dinger, LLC).

subfamilies. The zinc finger and H2TH motifs have been shown to be absolutely
necessary for Fpg to bind to DNA. 72,83,84 In addition to structural similarity, the
members of this superfamily exhibit a similar multistep catalytic mechanism that
generally involves a nucleophilic attack at the C1 0 position of the target nucleo-
tide by an N-terminal proline residue (in the case of Fpg, Nei, and NEIL1). 78,85
A comparison of these structures is discussed further below.