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Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease
Author(s) -
Tumbale Percy,
Schellenberg Matthew J,
Mueller Geoffrey A,
Fairweather Emma,
Watson Mandy,
Little Jessica N,
Krahn Juno,
Waddell Ian,
London Robert E,
Williams R Scott
Publication year - 2018
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.15252/embj.201798875
Subject(s) - biology , mechanism (biology) , microbiology and biotechnology , dna , biophysics , biochemistry , epistemology , philosophy
The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA ‐ DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 ( AOA 1). How APTX senses cognate DNA nicks and is inactivated in AOA 1 remains incompletely defined. Here, we report X‐ray structures of APTX engaging nicked RNA ‐ DNA substrates that provide direct evidence for a wedge‐pivot‐cut strategy for 5′‐ AMP resolution shared with the alternate 5′‐ AMP processing enzymes POL β and FEN 1. Our results uncover a DNA ‐induced fit mechanism regulating APTX active site loop conformations and assembly of a catalytically competent active center. Further, based on comprehensive biochemical, X‐ray and solution NMR results, we define a complex hierarchy for the differential impacts of the AOA 1 mutational spectrum on APTX structure and activity. Sixteen AOA 1 variants impact APTX protein stability, one mutation directly alters deadenylation reaction chemistry, and a dominant AOA 1 variant unexpectedly allosterically modulates APTX active site conformations.