Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats.

Nucleic Acids Research
Tariq MassadPål Stenmark

Abstract

As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the family of C proteins from P2-like bacteriophages. The structure reveals that the P2 C protein forms a symmetric dimer oriented to bind the major groove of two consecutive turns of the DNA. Surprisingly, P2 C has great similarities to binders of palindromic sequences. Nevertheless, the two identical DNA-binding helixes of the symmetric P2 C dimer have to bind different DNA sequences. Helix 3 is identified as the DNA-recognition motif in P2 C by alanine scanning and the importance for the individual residues in DNA recognition is defined. A truncation mutant shows that the disordered C-terminus is dispensable for repressor function. The short distance between the DNA-binding helices together with a possible interaction between two P2 C dimers are proposed to be responsible for extensive bending of the DNA. The structure provides insight into the mechanisms behind the mutants of P2 C causing dimer disruption, temperature...Continue Reading

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Citations

Dec 24, 2015·Journal of Biomolecular NMR·Tariq MassadPeter Damberg
Oct 13, 2015·Acta Crystallographica. Section F, Structural Biology Communications·Avisek MondalPradeep Parrack
May 5, 2016·Bacteriophage·Gail E Christie, Richard Calendar
Oct 11, 2015·FEBS Letters·Karin SkaarPål Stenmark

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Methods Mentioned

BETA
NMR
electrophoretic mobility shift assay
gel filtration
electrophoresis
gel-filtration

Software Mentioned

SCALA
Met
coot
Phenix Autosol
Se
MOLREP
MOSFLM
ARP
wARP
CCP4

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