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Georgia Tech

1. Watkins, Jason Derrick. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.

Degree: PhD, Chemistry and Biochemistry, 2008, Georgia Tech

The P22 c2 repressor protein (P22R) binds to DNA sequence-specifically and helps direct the temperate lambdoid bacteriophage P22 to the lysogenic developmental pathway. To gain insight into its DNA binding mechanism, we solved the 1.6 Å x-ray structure of the N-terminal domain (NTD) of P22R in a complex with a DNA fragment containing the synthetic operator sequence [d(ATTTAAGATATCTTAAAT)]2 This operator has an A-T at position 9L and T-A at position 9R and is termed DNA9T. Van der Waals interactions between protein and DNA appear to confer sequence-specificity. The structure of the P22R NTD – NA9T complex suggests that sequence-specificity arises substantially from interaction of a valine with a complementary binding cleft on the major groove surface of DNA9T. The cleft is formed by four methyl groups on sequential base pairs of 5' TTAA 3'. The valine cleft is intrinsic to the DNA sequence and does not arise from protein-induced DNA conformational change. Protein-DNA hydrogen bonding plays a secondary role in specificity. Advisors/Committee Members: Loren D. Williams (Committee Chair), Donald Doyle (Committee Member), Nicholas V. Hud (Committee Member), Roger Wartell (Committee Member), Stephen Harvey (Committee Member).

Subjects/Keywords: P22 repressor; Direct readout; Indirect readout; Protein binding; DNA-protein interactions; Van der Waals forces

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APA (6th Edition):

Watkins, J. D. (2008). X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/26709

Chicago Manual of Style (16th Edition):

Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Doctoral Dissertation, Georgia Tech. Accessed January 21, 2021. http://hdl.handle.net/1853/26709.

MLA Handbook (7th Edition):

Watkins, Jason Derrick. “X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout.” 2008. Web. 21 Jan 2021.

Vancouver:

Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Internet] [Doctoral dissertation]. Georgia Tech; 2008. [cited 2021 Jan 21]. Available from: http://hdl.handle.net/1853/26709.

Council of Science Editors:

Watkins JD. X-ray structures of p22 c2 repressor-dna complexes: the mechansism of direct and indirect readout. [Doctoral Dissertation]. Georgia Tech; 2008. Available from: http://hdl.handle.net/1853/26709

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