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Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage

Single-Molecule Dwell-Time Analysis of Restriction Endonuclease-Mediated DNA Cleavage

Published on: February 7, 2021

Structural analysis of DNA-protein complexes regulating the restriction-modification system Esp1396I.

Richard N A Martin¹, John E McGeehan, Neil J Ball

¹Institute of Biomedical and Biomolecular Science, University of Portsmouth, King Henry I Street, Portsmouth, Hampshire PO1 2DY, England.

Acta Crystallographica. Section F, Structural Biology and Crystallization Communications

|August 31, 2013

Summary

This summary is machine-generated.

The Esp1396I controller protein regulates gene expression by binding DNA. Unbound DNA naturally bends, and its major groove widens when bound by the protein, aiding complex formation.

Keywords:

DNA distortion DNA-binding proteins helix–turn–helix motif transcriptional regulation

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Area of Science:

Molecular Biology
Structural Biology
Genetics

Background:

Type II restriction-modification (RM) systems use controller proteins to regulate gene expression.
The Esp1396I RM system's controller protein (C-protein) binds distinct DNA operator sequences.
Previous studies detailed C-protein binding affinities to operator sites.

Purpose of the Study:

To investigate the structural basis of DNA bending in unbound operator sequences.
To elucidate the DNA structural changes induced by C-protein binding.
To understand the mechanism of cooperative binding in forming repression complexes.

Main Methods:

X-ray crystallography to obtain protein-DNA co-crystal structures.
Analysis of unbound DNA structures within protein-DNA complexes.
Comparative structural analysis of bound and unbound DNA states.

Main Results:

Two co-crystal structures of C-protein with portions of unbound DNA were determined.
Unbound DNA exhibited significant distortion and bending between conserved sequences.
Increased major groove width adjacent to bound C-protein dimers was observed.

Conclusions:

Naked operator DNA possesses an intrinsic propensity to bend.
DNA distortion facilitates cooperative binding of C-protein dimers.
Structural insights explain the formation of the tetrameric repression complex.