Journal Article

Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures

Yang, Haijuan, Pavletich, Nikola P., Chen, Zhucheng

2008

Overview

The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex. Here we have solved the crystal structures of the Escherichia coli RecA–ssDNA and RecA–heteroduplex filaments. They show that ssDNA and ATP bind to RecA–RecA interfaces cooperatively, explaining the ATP dependency of DNA binding. The ATP γ-phosphate is sensed across the RecA–RecA interface by two lysine residues that also stimulate ATP hydrolysis, providing a mechanism for DNA release. The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson–Crick-type base pairing. The complementary strand interacts primarily through base pairing, making heteroduplex formation strictly dependent on complementarity. The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling. DNA repair: Fair exchange One way of reversing DNA damage involves homologous pairing of an undamaged DNA with a damaged DNA, a process mediated by a class of proteins known as strand-exchange proteins. Chen et al . now present a 'holy grail' of the DNA repair field: the structure of the E. coli strand-exchange protein, RecA, bound to one and two DNA molecules. More than a dozen crystal structures of bacterial, archaebacterial and eukaryotic RecA-family members have been determined previously, but because RecA forms a filament on DNA, no crystal structures of RecA–DNA complexes were available. The new study avoids the problem of crystallizing a polymer by engineering RecA–DNA complexes that represent finite segments of the filament. DNA damage can be reversed by the homologous pairing of an undamaged DNA with a damaged DNA. Pavletich and colleagues report the structure of the E. coli strand-exchange protein, RecA, bound to DNA, offering new insight into the process by which homologous DNAs are paired.

• Publisher: Nature Publishing Group UK,Nature Publishing,Nature Publishing Group
• Subject: Adenosine Triphosphate - metabolism / Binding Sites / Biological and medical sciences / Crystalline structure / Crystallography, X-Ray / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - genetics / DNA - metabolism / DNA repair / DNA, Single-Stranded - chemistry / DNA, Single-Stranded - genetics / DNA, Single-Stranded - metabolism / E coli / Escherichia coli / Escherichia coli - enzymology / Escherichia coli - genetics / Fundamental and applied biological sciences. Psychology / Genetic diversity / Genic rearrangement. Recombination. Transposable element / Humanities and Social Sciences / Hydrogen bonds / Methods / Models, Molecular / Molecular and cellular biology / Molecular biophysics / Molecular genetics / multidisciplinary / Nucleic Acid Conformation / Nucleic Acid Heteroduplexes - chemistry / Nucleic Acid Heteroduplexes - genetics / Nucleic Acid Heteroduplexes - metabolism / Protein Conformation / Rec A Recombinases - chemistry / Rec A Recombinases - metabolism / Recombination, Genetic - genetics / Science / Science (multidisciplinary) / Sequence Homology, Nucleic Acid / Structure / Structure in molecular biology