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X-Ray Structures of P22 c2 Repressor-DNA Complexes: The Mechansism of Direct and Indirect Readout

by Watkins, Jason Derrick

Abstract (Summary)
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 DNA9T 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.
Bibliographical Information:

Advisor:Nicholas V. Hud; Donald Doyle; Loren D. Williams; Roger Wartell; Stephen Harvey

School:Georgia Institute of Technology

School Location:USA - Georgia

Source Type:Master's Thesis

Keywords:chemistry and biochemistry

ISBN:

Date of Publication:08/26/2008

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