The main focus of the Structure Function Group is to use X-ray crystallography to support research interest of principal investigators within the intramural community. Listed below are highlights from this past year. In collaboration with the Kunkel lab, we have been working on understanding the subtle differences of function between X family polymerases. In this review cycle, we published in Proceedings of the National Academy of Sciences on studies carried out on DNA polymerase Mu (Pol mu). Family X DNA polymerase mu is the only template-dependent human DNA polymerase known to participate in non-homologous end joining (NHEJ) of double strand DNA breaks whose 3ʹ-ends are not base paired. As such, Pol mu is involved in preserving gene sequence during immunoglobulin V(D)J recombination and plays a role in repair of DJH rearrangements during embryonic development and DNA breaks due to ionizing radiation. To better understand how Pol mu functions at the atomic level, we solved three crystals structures of the catalytic cycle of Pol mu filling a two nucleotide gap. Surprisingly, unlike polymerases lambda or beta (the other X family polymerases that can fill short gaps), Pol mu fills the gap by using the 5 end of the gap on the templating strand as the templating base in the nucleotidyl-transfer reaction. This is in sharp contrast to the other template dependent polymerases, which use the first available base on the 3 end of the gap as the templating base. This unique use of the templating strand provides insight into how Pol mu can function at a double strand break when the 3 end of the primer strand is unpaired. In this scenario, these structures suggests how Pol mu could use a templating base from the other end of the double strand break, creating microhomology at the break and allowing for ligation and subsequent repair of the double strand break. In collaboration with Drs Mueller and London at NIEHS, and Dr Pomes at INDOOR Biotechnologies we set out to investigate the potential cross reactivity of glutathione-S-transferase (GST) allergens from different species using structural biology and ELISA. For this study GSTs from cockroach (Bla g 5), helminth (Asc s 13), and two dust mite allergens (Der p 8 and Blo t 8) were compared, based on previous reports of cross reactivity in tropical climates. Crystal structures were solved of each of the four allergens. The results of the studies demonstrated that all GSTs presented similar overall dimeric structures, however there were few regions of contiguous exposed residues that might be responsible for cross reactivity among patients. This was consistent with the lack of significant cross-reactivity measured by ELISA amongst the 4 GSTs in a patient population from the temperate region of the North America. This demonstrated that each GST has unique antibodies. Therefore in patients, antibodies against the individual GST allergens can be used to accurately diagnose the sensitizing species in different regions. This work was published in the Journal of Allergy and Clinical Immunology.
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