Structure of an Aprataxin–DNA complex with insights into AOA1 Neurodegenerative Disease

DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5′-adenylation DNA damage (5′-AMP). Aprataxin (Aptx) catalyses direct reversal of 5′-AMP adducts to protect genome integrity. Here, the structure of an Aptx-DNA-AMP-Zn complex reveals active site and DNA interaction clefts formed by fusing a HIT (histidine triad) nucleotide hydrolase with an unprecedented DNA minor groove binding C(2)HE Zn-finger (Znf). An Aptx helical wedge interrogates the base stack for DNA end/nick sensing. HIT-Znf, the wedge, and an "[F/Y]PK" pivot motif cooperate to distort terminal DNA base-pairing and direct 5′-AMP into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5′-AMP adduct recognition and removal, and suggest mutations impacting protein folding, the active site pocket, and the pivot underlie Aptx dysfunction in the neurodegenerative disorder Ataxia Oculomotor Apraxia 1 (AOA1).