Structure of an aprataxin -DNA complex with insights into AOA1 neurodegenerative disease

Deficiencies in aprataxin, which reverses 5′-adenylate DNA adducts, can lead to the neurodegenerative disorder AOA1. Mutagenesis analyses and the crystal structure of the aprataxin ortholog from Schizosaccharomyces pombe in complex with DNA, AMP and Zn 2+ reveal the mechanisms by which this enzyme processes DNA lesions and maintains genome integrity. DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5′-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5′-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx–DNA–AMP–Zn 2+ complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove–binding C 2 HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5′-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5′-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).