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

@article{Chen2008MechanismOH,
  title={Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures},
  author={Zhucheng Chen and Haijuan Yang and Nikola P Pavletich},
  journal={Nature},
  year={2008},
  volume={453},
  pages={489-494}
}
The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. [] Key Method 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…
Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures
TLDR
Cryo-electron microscopy structures of the bacterial recombination protein RecA with DNA, and of RecA–D-loop complexes, provide insights into the double-stranded DNA opening, homology search and strand-exchange processes of homologous recombination.
The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination
TLDR
Structural and functional studies of the N-terminal domain (NTD) of the RecA protein suggest that the second function of NTD may be similar to that of Arg243 and Lys245, which were implicated earlier as binding sites of donor dsDNA.
Loop L 1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair
TLDR
The D161A-replacement of Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA- binding order in RecA-catalyzed recombinase reactions.
Complementary strand relocation may play vital roles in RecA-based homology recognition
TLDR
It is proposed that homology recognition is governed by transitions to and from the intermediate structure, where the transitions depend on differential extension in the dsDNA.
Structure/function relationships in RecA protein-mediated homology recognition and strand exchange
TLDR
A detailed discussion of structural features of the presynaptic filament that play important functional roles and includes many diagrams showing multiple filament turns that are not evident in single turn structures are provided.
RecO-mediated DNA homology search and annealing is facilitated by SsbA
TLDR
It is reported that RecO-mediated strand annealing is facilitated by cognate SsbA, but not by a heterologous one, and both proteins lose affinity for duplex DNA.
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments
TLDR
The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson–Crick pairing, and emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.
Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange
TLDR
Cryo-EM is used to solve the structures of human RAD51 in complex with DNA molecules, in presynaptic and postsynaptic states, at near-atomic resolution, and reveals both conserved and distinct structural features of the human RAD 51–DNA complexes compared with their prokaryotic counterpart.
Dynamics of Protein–ssDNA Interactions in the Bacteriophage T4 Homologous Recombination System
TLDR
Current models for the assembly and dynamic instability of the T4 presynaptic filament are explored and how mechanistic features of this system may be conserved in other recombination systems are shown.
...
...

References

SHOWING 1-10 OF 58 REFERENCES
The mutant RecA proteins, RecAR243Q and RecAK245N, exhibit defective DNA binding in homologous pairing.
TLDR
The results suggest that the region including Arg243 and Lys245 may be involved in the path of secondary DNA binding to the presynaptic filament.
Structure and mechanism of Escherichia coli RecA ATPase
  • C. Bell
  • Chemistry, Biology
    Molecular microbiology
  • 2005
TLDR
A unifying theme is emerging for RecA and related ATPase enzymes in which the binding of ATP at a subunit interface results in large conformational changes that are coupled to interactions with the substrates in such a way as to promote the desired reactions.
The Bacterial RecA Protein: Structure, Function, and Regulation
TLDR
The bacterial RecA protein is the prototypical recombinase, promoting the central steps of DNA pairing and strand exchange in genetic recombination and recombinational DNA repair, and plays a direct role in the UV mutagenesis promoted by DNA polymerase V.
The function of the secondary DNA‐binding site of RecA protein during DNA strand exchange
TLDR
It is demonstrated that single‐stranded DNA‐binding protein can sequester ssDNA, preventing its binding to the secondary site and thereby assisting at two levels: it averts the inhibition caused by an excess of ssDNA and prevents the reversal of DNA strand exchange by removing the displaced strand from thesecondary site.
The helicity of DNA in complexes with RecA protein
TLDR
The present work determines the helicity of DNA in the recA complex and finds that the DNA helix follows the protein helix visible in the electron microscope and has 18.6 bp per turn, which corresponds to an unwinding of the DNA double helix by 15° per bp.
Similarity of the yeast RAD51 filament to the bacterial RecA filament.
The RAD51 protein functions in the processes of DNA repair and in mitotic and meiotic genetic recombination in the yeast Saccharomyces cerevisiae. The protein has adenosine triphosphate-dependent DNA
The bacterial RecA protein and the recombinational DNA repair of stalled replication forks.
TLDR
New biochemical and structural information highlights both the similarities and distinctions between RecA and its homologs, and increasingly, those differences can be rationalized in terms of biological function.
Direct observation of individual RecA filaments assembling on single DNA molecules
TLDR
The direct observation of filament assembly on individual double-stranded DNA molecules using fluorescently modified RecA indicates that assembly in vivo is controlled at the nucleation step, in accord with extensive genetic and biochemical studies.
...
...