Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes

Abstract

Background: DNA apurinic/apyrimidinic (AP) sites are toxic and mutagenic if unrepaired by AP endonucleases. Results: Structural, mutational, and computational analyses of prototypic AP endonucleases APE1 and Nfo identify surprising similarities. Conclusion: APE1 and Nfo reveal functional equivalences illuminating their catalytic reaction. Significance: A conserved catalytic geometry is specific to AP site removal despite different enzyme structures and metal ions.

Human Apurinic/Apyrimidinic Endonuclease 1

“…Other important residues include N68, D70, Y171, N212, D283, and D308, which are generally conserved throughout the diverse members of the phosphoesterase superfamily. Still, further studies are needed to delineate the precise catalytic reaction mechanism, which is debated in several recent publications (123,148,152,210).…”

DNA damage and base excision repair : an important role during zebrafish embryogenesis

“…The authors claimed that, based on the distances and angles between individual residues and DNA atoms at the AP site, many of the actions outlined above, particularly those of the tyrosine residues, are not consistent with their structure. However, the authors do not propose any new models or insight into the functionality of Apex1 (Tsutakawa et al 2013). …”

“…For example, all crystal structures to date for Apex1 show that Cys 65 is buried deep within the protein; this observation is supported by proteolysis experiments (Strauss and Holt 1998). Access to Cys 65 would require extensive remodelling, evidence for which is currently lacking, nor has any mechanism to make the various cysteines accessible been proposed (Georgiadis et al 2008;Tsutakawa et al 2013). Although Apex1 knockout is embryonic lethal at ~E8.6 in mice, when Cys 64 (equivalent to human Cys 65 ) was mutated to alanine in mouse embryos the embryos develop normally and there is no difference in DNA binding of Fos, Jun or AP-1, indicating that either Cys 64 was not involved in the redox activity of Apex1, or redox activity as a whole was not an essential function (Ordway, Eberhart, and Curran 2003).…”

“…Structurally Apex1 is a globular α/β protein comprising a two-layered six-stranded β-sheet core flanked by α-helices, while the Nterminal domain, comprised of the first 45 amino acids, is disordered. Additionally, Apex1 is Mg 2+ -dependent (Mol et al 1995;Strauss and Holt 1998;Tsutakawa et al 2013). …”

“…The start codon is in the second exon and most cross-species homology is in the fifth exon (Robson et al 1992). The Apex1 protein is comprised of a highly conserved C-terminal nuclease domain, responsible for the DNA repair function, attached to an N-terminus that is not conserved across phyla (Tsutakawa et al 2013;Wilson and Simeonov 2010). Structurally Apex1 is a globular α/β protein comprising a two-layered six-stranded β-sheet core flanked by α-helices, while the Nterminal domain, comprised of the first 45 amino acids, is disordered.…”