Co-authors (L to R) David Jeruzalmi, Danaya Pakotiprapha, and Gregory L. Verdine
Genomic DNA is under constant attack by various damaging agents, both endogenous such as reactive oxygen species generated in the cells during metabolism, and exogenous such as UV radiation and carcinogens in our food and environment. Left uncorrected, such damage can lead to mutations that are deleterious. Cells have evolved many DNA repair pathways to counteract these DNA lesions. One of these repair pathways is called nucleotide excision repair (NER). NER is interesting because it can recognize and repair a wide range of structurally unrelated types of DNA damage. Conserved throughout evolution, NER involves three major steps: damage recognition, incision, and repair synthesis. In bacteria, the damage recognition step is carried out by two proteins called UvrA and UvrB.
Important progress on understanding the molecular aspects of NER was recently reported in the January 18 issue of the journal Molecular Cell by Harvard graduate students Danaya Pakotiprapha (Molecular and Cellular Biology (MCB) Department) and Yoshihiko Inuzuka (Department of Chemistry and Chemical Biology (CCB)) working with Professors David Jeruzalmi (MCB) and Gregory Verdine (CCB) at Harvard. Specifically, they determined the first crystal structure of UvrA from the bacterium Bacillus stearothermophilus. UvrA belongs to the ATP-binding cassette (ABC) superfamily of ATPases and plays a key role in initial damage recognition. The structure reveals how ATP, the cellular fuel, regulates dimerization of UvrA in a manner that differs from that observed in other ABC ATPases. The crystallographic model and calculations of surface properties and sequence conservation were used to design biochemical experiments that allowed the workers to determine the UvrA surface that is used in the interaction with UvrB, its partner in damage recognition, and the likely path for DNA binding during the search for lesion in the DNA.
This analysis provides a framework for interpreting the biochemistry of UvrA in structural terms and a basis for future experiments aimed at a deeper understanding of how NER can repair a wide range of structurally unrelated DNA lesions.