NDLI: Origins of DNA-binding specificity: role of protein contacts with the DNA backbone.

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Origins of DNA-binding specificity: role of protein contacts with the DNA backbone.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Karzai, A. W. Schildbach, J. F. Sauer, R. T. Raumann, B. E.
Description	Author Affiliation: Schildbach JF ( Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA.);
Abstract	A central question in protein-DNA recognition is the origin of the specificity that permits binding to the correct site in the presence of excess, nonspecific DNA. In the P22 Arc repressor, the Phe-10 side chain is part of the hydrophobic core of the free protein but rotates out to pack against the sugar-phosphate backbone of the DNA in the repressor-operator complex. Characterization of a library of position 10 variants reveals that Phe is the only residue that results in fully active Arc. One class of mutants folds stably but binds operator with reduced affinity; another class is unstable. FV10, one member of the first class, binds operator DNA and nonoperator DNA almost equally well. The affinity differences between FV10 and wild type indicate that each Phe-10 side chain contributes 1.5-2.0 kcal to operator binding but less than 0.5 kcal/mol to nonoperator binding, demonstrating that contacts between Phe-10 and the operator DNA backbone contribute to binding specificity. This appears to be a direct contribution as the crystal structure of the FV10 dimer is similar to wild type and the Phe-10-DNA backbone interactions are the only contacts perturbed in the cocrystal structure of the FV10-operator complex.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	3
Volume Number	96
Language	English
Publisher	National Academy of Sciences
Publisher Date	1999-03-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	DNA-Binding Proteins Chemistry Metabolism DNA Protein Structure, Secondary Repressor Proteins Viral Proteins Amino Acid Sequence Binding Sites Cloning, Organism Crystallography, X-Ray Dimerization Escherichia Coli Kinetics Models, Molecular Molecular Sequence Data Mutagenesis, Insertional Mutagenesis, Site-Directed Nucleic Acid Conformation Peptide Library Substrate Specificity Viral Regulatory And Accessory Proteins Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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