Among DNA repair pathways, nucleotide excision repair (NER) is unique in its ability to recognize and remove a wide variety of structurally unrelated DNA lesions. NER is a multi-step, ATP-dependent process that involves three major steps: damage recognition, incision, and repair synthesis. In bacteria, the damage recognition and incision steps are carried out by three proteins: UvrA, UvrB, and UvrC.

The crystal structure and biochemical studies of Bacillus stearothermophilus UvrA presented in this thesis provide molecular understanding of the ATP-modulated dimerization of UvrA, as well as the interaction with DNA and UvrB, its partner in lesion recognition.

Although the structure of the 5' endonuclease domain of UvrC was solved in the absence of DNA substrate and did not contain bound metal ions, comparison of our structure with the structure of Bacillus halodurans RNase HI, which was determined in complex with an RNA-DNA hybrid and two divalent metal ions, allowed us to propose a two-metal-ion mechanism for the 5' incision by UvrC. This proposed mechanism is well supported by the available biochemical data.

Biochemical and biophysical characterization of the BstUvrAB and BstUvrA·DNA complexes are also reported. It was observed that formation of the BstUvrAB complex is promoted by ATP binding, but not hydrolysis. Formation of a stable BstUvrA·DNA complex requires at least ∼30 bp of DNA, consistent with DNase I footprinting results. Although both BstUvrAB and BstUvrA·DNA complexes could be formed in large quantities and have been subjected to crystallization trials, no well diffracting crystals have been obtained.

Biochemical characterizations of NER proteins from several bacterial species revealed that the NER systems in different bacteria can be quite divergent, and that the proteins from different species are not functionally interchangeable. More complete understanding of nucleotide excision repair awaits further studies in a larger number of bacterial systems.