Mutational and Kinetic Analysis of APE1 Endoribonuclease Activity

A A Kuznetsova; A A Gavrilova; D S Novopashina; O S Fedorova; N A Kuznetsov

doi:10.1134/S0026893321020102

Mutational and Kinetic Analysis of APE1 Endoribonuclease Activity

Mol Biol. 2021;55(2):211-224. doi: 10.1134/S0026893321020102. Epub 2021 Apr 29.

Authors

A A Kuznetsova¹, A A Gavrilova^{1

2}, D S Novopashina¹, O S Fedorova¹, N A Kuznetsov¹

Affiliations

¹ Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
² Novosibirsk National Research State University, 630090 Novosibirsk, Russia.

Abstract

Human apurinic/apyrimidinic endonuclease 1 (APE1) participates in the DNA repair system. It is believed that the main biological function of APE1 is Mg²⁺-dependent hydrolysis of AP-sites in DNA. On the base of structural data, kinetic studies, and mutation analysis, the key stages of APE1 interaction with damaged DNA were established. It has been shown recently that APE1 can act as an endoribonuclease that catalyzes mRNA hydrolysis at certain pyrimidine-purine sites and thus controls the level of certain transcripts. In addition, the presence of Mg²⁺ ions was shown to be not required for the endoribonuclease activity of APE1, in contrast to the AP-endonuclease activity. This indicates differences in mechanisms of APE1 catalysis on RNA and DNA substrates, but the reasons for these differences remain unclear. Here, the analysis of endoribonuclease hydrolysis of model RNA substrates with wild type APE1 enzyme and its mutant forms Y171F, R177F, R181A, D210N, N212A, T268D, M270A, and D308A, was performed. It was shown that mutation of Asn212, Asp210, and Tyr171 residues leads to the decrease of AP-endonuclease activity while endoribonuclease activity is retained. Also, T268D and M270A APE1 mutants lose specificity to pyrimidine-purine sequences. R177F and R181A did not show a significant decrease in enzyme activity, whereas D308A demonstrated a decrease of endoribonuclease activity.

Keywords: APE1; RNA substrates; active site; endoribonuclease activity; human apurine/apyrimidine endonuclease; site-directed mutagenesis.

© Pleiades Publishing, Inc. 2021, ISSN 0026-8933, Molecular Biology, 2021, Vol. 55, No. 2, pp. 211–224. © Pleiades Publishing, Inc., 2021.Russian Text © The Author(s), 2021, published in Molekulyarnaya Biologiya, 2021, Vol. 55, No. 2, pp. 243–257.