ruvatx

I. Introduction

Homologous recombination is vastly important in the generation of genetic diversity and in DNA repair in all organisms. A crucial step in recombination is the resolution of Holliday junctions, which form as a result of strand exchange between two homologous DNA helices:

After the formation of Holliday intermediates, the length of heteroduplex DNA may be extended through the process of branch migration, and the Holliday junction can be topologically rearranged into a "chi" structure:

In Escherichia coli, branch migration and resolution of Holliday junctions to produce two, separate, intact DNA helices is accomplished by a suite of proteins: RuvA, RuvB, and RuvC.

RuvA binds as a tetramer to the Holliday junction, followed by loading of RuvB, which acts as a molecular motor to drive branch migration. RuvC then acts to cleave the junction and resolve the two DNA molecules into mature recombination products.

At left is shown an RuvA tetramer bound to DNA oligonucleotides representing a Holliday junction (chi structure, with partial heteroduplex regions indicated).

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The RuvA monomer has an "L" shape, composed of three domains: I, II, III. The loop connecting domain II and domain III is not shown.

Domain I is a six-stranded, anti-parallel beta barrel, whereas both domains II and III consist entirely of alpha helices.

In tetrameric RuvA, each monomer is a lobe of the symmetrical tetramer. Domain I of each monomer is positioned centrally, and domains II and III are located peripherally.

Examining the charge distribution of atoms over the surface of the RuvA tetramer, it is clear that the DNA binding surface is largely positively charged (basic), whereas the opposite surface is largely negatively charged (acidic). The yellow, orange, and red colors represent relatively negatively charged atoms and the green and blue colors represent more positively charged atoms (acidic residues and basic residues are colored in their entirety). The relative positive charge of the DNA binding surface attracts the negatively charged DNA backbone.

An exception to the mostly basic surface of the DNA binding side of the RuvA tetramer is an eight residue acidic central pin comprising glutamate⁵⁵ and aspartate⁵⁶ of each monomer. This negatively charged center may repel the negatively charged oxygens of the DNA backbone, driving the DNA away from the center of the Holliday junction.

A number of residues that interact directly or indirectly (via water molecules) with the DNA backbone line the channels in which Holliday junction DNA is bound.