PDBsum entry 2rph

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PDB id:
Name: DNA
Title: Rect-bound ssdna
Structure: DNA (5'-d( Dtp Dap Dcp Dg)-3'). Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: nucleotide synthesis
NMR struc: 10 models
Authors: T.Masuda,Y.Ito,T.Shibata,T.Mikawa
Key ref:
T.Masuda et al. (2009). A non-canonical DNA structure enables homologous recombination in various genetic systems. J Biol Chem, 284, 30230-30239. PubMed id: 19729448 DOI: 10.1074/jbc.M109.043810
15-May-08     Release date:   26-May-09    


DOI no: 10.1074/jbc.M109.043810 J Biol Chem 284:30230-30239 (2009)
PubMed id: 19729448  
A non-canonical DNA structure enables homologous recombination in various genetic systems.
T.Masuda, Y.Ito, T.Terada, T.Shibata, T.Mikawa.
Homologous recombination, which is critical to genetic diversity, depends on homologous pairing (HP). HP is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. This expansion unavoidably causes untwisting of the parental double-stranded DNA. RecA/Rad51-catalyzed ATP-dependent HP is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. However, in vivo, double-stranded DNA is relaxed by bound proteins and thus is an unfavorable substrate for RecA/Rad51. In contrast, Mhr1, an ATP-independent HP protein required for yeast mitochondrial homologous recombination, catalyzes HP without the net untwisting of double-stranded DNA. Therefore, we questioned whether Mhr1 uses a novel strategy to promote HP. Here, we found that, like RecA, Mhr1 induced the extension of bound single-stranded DNA. In addition, this structure was induced by all evolutionarily and structurally distinct HP proteins so far tested, including bacterial RecO, viral RecT, and human Rad51. Thus, HP includes the common non-canonical DNA structure and uses a common core mechanism, independent of the species of HP proteins. We discuss the significance of multiple types of HP proteins.
  Selected figure(s)  
Figure 4.
Comparison of the solution and crystal structures of ssDNA bound to RecA.A, superimposition of the solution structure of RecA-d(TACG) (19) (in magenta) and four DNA residues in the RecA[5]-(dT)[15] crystal structure (21) (in cyan). The crystal structure is similar to the solution structure. D1, D2, and D3 indicate distances between adjacent bases (see also Table 1). Inset, the orientation of adjacent bases showing only the base groups. B, the ssDNA structure in the RecA[5]-(dT)[15] crystal structure. Each triplet is colored orange, yellow, and green. Three binding modes of d(TACG) to the RecA filament based on the crystal structure (models 1, 2, and 3). The best ratio for each of these models is shown below. C, van der Waals contacts between adjacent bases of B-form and RecA-bound ssDNA. B-form ssDNA (in green), ssDNA from the crystal structure of the RecA[5]·(dT)[15] complex (in cyan), and the solution structure of d(TACG) bound to RecA (in magenta). van der Waals contacts between the surfaces of N1, C2, N3, C4, C5, C6, N7, C8, and N9 are shown by dots.
Figure 5.
Model images of HP protein-bound DNA.A, ecRecA-bound ssDNA. B–F, ecRecA-, hsRad51-, ecRecT-, ttRecO-, and Mhr1-bound ssDNA in which H2″ of the 5′-residue is replaced by a hydroxyl group. The H2″ (A) and hydroxyl group (B–F) of the 5′-residue are represented by space-filling (dark gray). A base and sugar-ring of the second residue are also represented by space-filling (light gray).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 30230-30239) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20581116 C.Manfredi, Y.Suzuki, T.Yadav, K.Takeyasu, and J.C.Alonso (2010).
RecO-mediated DNA homology search and annealing is facilitated by SsbA.
  Nucleic Acids Res, 38, 6920-6929.  
20308162 L.T.Chen, and A.H.Wang (2010).
A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo.
  Nucleic Acids Res, 38, 4361-4371.  
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