Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair

Lee, Byung Il; Kim, Kyoung Hoon; Park, Soo-Jeong; Eom, Soo Hyun; Song, Hyun Kyu; Suh, Se Won

doi:10.1038/sj.emboj.7600222

Cited by 108 publications

(145 citation statements)

References 68 publications

(87 reference statements)

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“…The manner in which RecR proteins bind DNA has not been well described, although the drRecR tetramer has been reported to bind both dsDNA and ssDNA (22). The dsDNA binding of the RecR dimer could not be observed by a gel retardation analysis (Fig.…”

Section: Discussionmentioning

confidence: 92%

“…However, the two aspartate residues are not conserved in the Toprim domain of RecR (35). Recently, structural analysis of drRecR showed that the RecR Toprim domain commonly has a RecR-specific acidic cluster region that consists of three acidic residues (Glu-84, Asp-88, and Glu-144 in the case of T. thermophilus RecR) (22). In this study, we used NMR titration analysis to reveal that the Toprim domain of RecR is not involved in DNA binding through Mg 2ϩ .…”

Section: Discussionmentioning

confidence: 99%

“…In contrast, the crystallized drRecR formed a ring-like tetramer in which N-terminal HhH motifs (1-53 residues) contacted with each other and C-terminal regions (175-198 residues) swapped as described in Fig. 1B (22).…”

Section: Prediction Of Ttrecr Dimer Structure By Homology Modeling-mentioning

confidence: 99%

“…For homology modeling calculations, the drRecR structure was obtained from the Protein Data Bank, 1VDD (22). The integrity and quality of the models were assessed using the program PRO-CHECK, which generates Ramachandran plot of model structure.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, RecR is thought to be the key mediator of RecF and RecO association at dsDNAssDNA junctions. The crystal structure of Deinococcus radiodurans RecR (drRecR) was recently determined (22). As predicted from sequence analysis, drRecR consists of a helix-hairpin-helix (HhH) motif, a zinc finger motif, a Toprim domain, and a Walker B motif.…”

mentioning

confidence: 99%

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Identification of the RecR Toprim Domain as the Binding Site for both RecF and RecO

Honda

Inoue

Yoshimasu

et al. 2006

Journal of Biological Chemistry

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The RecR protein forms complexes with RecF or RecO that direct the specific loading of RecA onto gapped DNA. However, the binding sites of RecF and RecO on RecR have yet to be identified. In this study, a Thermus thermophilus RecR dimer model was constructed by NMR analysis and homology modeling. NMR titration analysis suggested that the hairpin region of the helix-hairpin-helix motif in the cavity of the RecR dimer is a binding site for double-stranded DNA (dsDNA) and that the acidic cluster region of the Toprim domain is a RecO binding site. Mutations of Glu-84, Asp-88, and Glu-144 residues comprising that acidic cluster were generated. The E144A and E84A mutations decreased the binding affinity for RecO, but the D88A did not. Interestingly, the binding ability to RecF was abolished by E144A, suggesting that the region surrounding the RecR Glu-144 residue could be a binding site not only for RecO but also for RecF. Furthermore, RecR and RecF formed a 4:2 heterohexamer in solution that was unaffected by adding RecO, indicating a preference by RecR for RecF over RecO. The RecFR complex is considered to be involved in the recognition of the dsDNA-ssDNA junction, whereas RecO binds single-stranded DNA (ssDNA) and ssDNA-binding protein. Thus, the RecR Toprim domain may contribute to the RecO interaction with RecFR complexes at the dsDNA-ssDNA junction site during recombinational DNA repair mediated by the RecFOR.Maintaining genomic integrity by repairing damaged DNA is crucial for all organisms. DNA damage can arise during normal DNA metabolism such as the introduction of mismatches during replication and the deamination of bases, or it can be caused by exposure to exogenous factors such as ultraviolet radiation, ␥-radiation, and chemical mutagens. Such DNA damage is mostly repaired by base excision repair, nucleotide excision repair, and mismatch repair pathways, based on information provided by the complementary strand in a damaged duplex. However, double-stranded DNA (dsDNA) 2 break and base lesions in single-stranded DNA (ssDNA) gap regions having no complementary strands can also arise, mainly during replication. To cope with this category of DNA damage, organisms have developed recombinational repair pathways that minimize the loss of genetic information by using homologous DNA as a template for repair.RecFOR and/or RecBCD pathways are required to initiate homologous DNA recombination in bacteria (1). The Escherichia coli RecFOR pathway is mainly used for ssDNA gap repair, whereas the RecBCD pathway is responsible for dsDNA break repair. However, the RecFOR pathway can also repair dsDNA breaks, as has been demonstrated in recBC sbcB mutants, which are deficient in the RecBCD pathway (2, 3). In the RecFOR pathway, dsDNA breaks are unwound by the RecQ helicase and processed by the RecJ 5Ј-to 3Ј-exonuclease, and the resulting 3Ј-tailed ssDNA is coated with the ssDNA-binding protein (SSB). The RecF, RecO, and RecR proteins then mediate the loading of RecA protein onto the SSB-coated ssDNA, specifically at junctio...

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Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Prediction Of Ttrecr Dimer Structure By Homology Modeling-mentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Identification of the RecR Toprim Domain as the Binding Site for both RecF and RecO

Honda

Inoue

Yoshimasu

et al. 2006

Journal of Biological Chemistry

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An Introduction to the Mechanical Bond

Bruns¹

2016

The Nature of the Mechanical Bond

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Catenane: fünfzig Jahre molekulare Verschlingungen

2015

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Ein halbes Jahrhundert nach der ersten gerichteten Synthese eines [2]Catenans durch Schill und Lüttringhaus existiert heutzutage eine Vielzahl an Strategien zur Synthese von Hopf‐Verschlingungen (einfach verzahnten Ringen), der einfachsten Klasse der Catenane. Die Präzision und Effektivität, mit der geeignete Template und/oder nichtkovalente Wechselwirkungen Bausteine anordnen können, ermöglichten die Synthese komplizierter – und häufig schöner – verzahnter Systeme höherer Ordnung, darunter Salomonische Verschlingungen, Borromäische Ringe und ein Davidstern‐Catenan. In diesem Aufsatz werden die zahlreichen Strategien, die im 21. Jahrhundert zur Synthese von Catenanen zur Verfügung stehen, vorgestellt und potenzielle Anwendungen untersucht. Des Weiteren werden die Herausforderungen bei der Synthese noch komplizierterer Topologien aufgezeigt.

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Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair

Cited by 108 publications

References 68 publications

Identification of the RecR Toprim Domain as the Binding Site for both RecF and RecO

Identification of the RecR Toprim Domain as the Binding Site for both RecF and RecO

An Introduction to the Mechanical Bond

Catenane: fünfzig Jahre molekulare Verschlingungen

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