Structural Biology of Genome Maintenance and DNA repair

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With combined biochemical, mutational, and protein structural analyses (eg. X-ray crystallography and Small angle X-ray scattering), we dissect functionally critical protein conformations, protein-protein and protein-nucleic acid interfaces. We are currently focused on examining structure/function of DNA end processing factor Aprataxin (APTX). APTX is a conserved eukaryotic DNA repair enzyme that is important for protection of cells from oxidative DNA damage, and APTX mutations cause the recessive hereditary neurodegenerative disorder Ataxia with Oculomotor Apraxia 1 (AOA1). In the ultimate step of DNA replication and repair processes, DNA ligases seal DNA nicks through an imperfect mechanism that can abort when the ligase encounters DNA termini harboring the products of oxidative or DNA-alkylation damage. Such "abortive ligation" generates a secondary form of damage, 5'-adenylated DNA-termini, which are corrected by APTX to protect genomic integrity. However, due to a lack of protein structural information, the molecular basis for APTX catalytic reversal of 5' adenylation damage, and how APTX is inactivated in the neurodegenerative disorder Ataxia with Oculomotor Apraxia 1 (AOA1) remain largely unknown. Towards understanding APTX mechanism we have developed robust overexpression systems for human and yeast aprataxin homologs and we aim to define molecular determinants of APTX DNA repair, and how APTX integrates into damage repair pathways through interactions with DNA break repair pathways through binding Xrcc1 (DNA single strand break repair, SSBR) and Xrcc4 (DNA double strand break repair, DSBR). We are specifically testing hypotheses that: 1) APTX Histidine triad (HIT) and Zinc finger (Znf) domains form a composite fused catalytic domain for DNA structure specific nick-binding, 5'-AMP recognition, and DNA-deadenylation processing, 2) AOA1 patient mutations disrupt APTX protein folding and/or directly impair APTX catalytic activities through active site distortion, and 3) The FHA domain and FHA-HIT linker provides a flexible leash targeting APTX DNA deadenylation activity to Caesin kinase 2 (CK2) phosphorylated XRCC4 and XRCC1 DNA repair scaffolds. Ionizing radiation (IR) and non-ionizing radiation from exogenous natural sources such as cosmic rays, radioactive elements in the environment, or from artificial sources including diagnostic X-rays mount a constant assault our genomes. Oxidative DNA damage from reactive oxygen species generated as by-products of mitochondrial respiration, during chronic inflammation, or upon exposure to environmental agents poses a threat to all cell types. Thus our knowledge of the DNA SSBR and DSBR repair mechanisms we are studying has critical implications for environmental health. Significantly, DNA repair defects underpin many human diseases associated with disorders of the nervous system and we are working to understand how heritable DNA repair defects impair damage surveillance and contribute to neurodegeneration.