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PDBsum entry 1i1v
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Deoxyribonucleic acid PDB id
1i1v

 

 

 

 

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Contents
DNA/RNA
Theoretical model
PDB id:
1i1v
Name: Deoxyribonucleic acid
Title: A theoretical model of triple-stranded DNA bound to reca protein (n-s interconversion model)
Structure: 5'-d(p Gp Gp G)-3'. Chain: a. Engineered: yes. 5'-d(p Cp Cp C)-3'. Chain: b, c. Engineered: yes
Source: Synthetic: yes. Synthetic: yes
Authors: T.Nishinaka,A.Shinohara,Y.Ito,S.Yokoyama,T.Shibata
Key ref:
T.Nishinaka et al. (1998). Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination. Proc Natl Acad Sci U S A, 95, 11071-11076. PubMed id: 9736691 DOI: 10.1073/pnas.95.19.11071
Date:
04-Feb-01     Release date:   21-Feb-01    
 Headers
 References

DNA/RNA chains
  G-G-G 3 bases
  C-C-C 3 bases
  C-C-C 3 bases

 

 
DOI no: 10.1073/pnas.95.19.11071 Proc Natl Acad Sci U S A 95:11071-11076 (1998)
PubMed id: 9736691  
 
 
Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination.
T.Nishinaka, A.Shinohara, Y.Ito, S.Yokoyama, T.Shibata.
 
  ABSTRACT  
 
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Base rotation by interconversion of sugar puckers. (a) Top view of the base rotation caused by interconversion of the sugar puckers. The sugar pucker of the 5'-residue (T, top) is in the S-type (Left) and the N-type (Right), whereas that of the 3'-residue (A, bottom) is fixed in the S-type. Note that the hydrogen-bonding vector is rotated toward its major groove by the conversion from the S-type to the N-type. (b) Two types of deoxyribose-base stacking. All residues are in the S-type sugar pucker (Left) or the N-type (Right) sugar pucker. 		Figure 4.
Fig. 4. A three-stranded DNA model for homology search and strand exchange considering the N-S interconversion of sugar puckers. (a) A molecular model of base pair switch between single- and double-stranded DNA. The bottom three residues are in the N-type and the top three residues are in the S-type. Note that the base pairing is altered by the conversion of sugar puckers between the N- and S-type. (b) Base rotation schemes for base pair switching against the interconversion of the sugar puckers. The bases are rotated toward the minor groove when the sugar puckers are converted from the N-type (Left) to the S-type (Right) and toward the major groove with the opposite (S-type to N-type) conversion.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21483664 J.Miné-Hattab, G.Fleury, C.Prevost, M.Dutreix, and J.L.Viovy (2011).
Optimizing the design of oligonucleotides for homology directed gene targeting.
  PLoS One, 6, e14795.  
19193646 F.Ling, M.Yoshida, and T.Shibata (2009).
Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase.
  J Biol Chem, 284, 9341-9353.  
19729448 T.Masuda, Y.Ito, T.Terada, T.Shibata, and T.Mikawa (2009).
A non-canonical DNA structure enables homologous recombination in various genetic systems.
  J Biol Chem, 284, 30230-30239.
PDB codes: 2rpd 2rpe 2rpf 2rph
18953036 G.Lahoud, K.Arar, Y.M.Hou, and H.Gamper (2008).
RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine.
  Nucleic Acids Res, 36, 6806-6815.  
17523678 N.Mazloum, Q.Zhou, and W.K.Holloman (2007).
DNA binding, annealing, and strand exchange activities of Brh2 protein from Ustilago maydis.
  Biochemistry, 46, 7163-7173.  
16549875 A.Kegel, P.Martinez, S.D.Carter, and S.U.Aström (2006).
Genome wide distribution of illegitimate recombination events in Kluyveromyces lactis.
  Nucleic Acids Res, 34, 1633-1645.  
16847846 J.Xiao, A.M.Lee, and S.F.Singleton (2006).
Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination.
  Chembiochem, 7, 1265-1278.  
16909421 M.Petukhov, D.Lebedev, V.Shalguev, A.Islamov, A.Kuklin, V.Lanzov, and V.Isaev-Ivanov (2006).
Conformational flexibility of RecA protein filament: transitions between compressed and stretched states.
  Proteins, 65, 296-304.  
15749781 R.Fulconis, M.Dutreix, and J.L.Viovy (2005).
Numerical investigation of sequence dependence in homologous recognition: evidence for homology traps.
  Biophys J, 88, 3770-3779.  
14739235 A.K.Shchyolkina, D.N.Kaluzhny, O.F.Borisova, M.E.Hawkins, R.L.Jernigan, T.M.Jovin, D.J.Arndt-Jovin, and V.B.Zhurkin (2004).
Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin.
  Nucleic Acids Res, 32, 432-440.  
15205482 B.Bi, N.Rybalchenko, E.I.Golub, and C.M.Radding (2004).
Human and yeast Rad52 proteins promote DNA strand exchange.
  Proc Natl Acad Sci U S A, 101, 9568-9572.  
15383285 E.Folta-Stogniew, S.O'Malley, R.Gupta, K.S.Anderson, and C.M.Radding (2004).
Exchange of DNA base pairs that coincides with recognition of homology promoted by E. coli RecA protein.
  Mol Cell, 15, 965-975.  
15698024 K.D.Dorfman, R.Fulconis, M.Dutreix, and J.L.Viovy (2004).
Model of RecA-mediated homologous recognition.
  Phys Rev Lett, 93, 268102.  
15345529 K.Klapstein, T.Chou, and R.Bruinsma (2004).
Physics of RecA-mediated homologous recognition.
  Biophys J, 87, 1466-1477.  
12514138 P.Noirot, R.C.Gupta, C.M.Radding, and R.D.Kolodner (2003).
Hallmarks of homology recognition by RecA-like recombinases are exhibited by the unrelated Escherichia coli RecT protein.
  EMBO J, 22, 324-334.  
12453425 M.Frank-Vaillant, and S.Marcand (2002).
Transient stability of DNA ends allows nonhomologous end joining to precede homologous recombination.
  Mol Cell, 10, 1189-1199.  
11600714 S.J.Shi, A.Scheffer, E.Bjeldanes, M.A.Reynolds, and L.J.Arnold (2001).
DNA exhibits multi-stranded binding recognition on glass microarrays.
  Nucleic Acids Res, 29, 4251-4256.  
11459985 T.Shibata, T.Nishinaka, T.Mikawa, H.Aihara, H.Kurumizaka, S.Yokoyama, and Y.Ito (2001).
Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material.
  Proc Natl Acad Sci U S A, 98, 8425-8432.  
11106508 H.B.Gamper, Y.M.Hou, and E.B.Kmiec (2000).
Evidence for a four-strand exchange catalyzed by the RecA protein.
  Biochemistry, 39, 15272-15281.  
11088561 H.Zhou, Y.Zhang, and Z.Ou-Yang (2000).
Elastic property of single double-stranded DNA molecules: theoretical study and comparison with experiments.
  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 62, 1045-1058.  
10956007 K.P.Rice, J.C.Chaput, M.M.Cox, and C.Switzer (2000).
RecA protein promotes strand exchange with DNA substrates containing isoguanine and 5-methyl isocytosine.
  Biochemistry, 39, 10177-10188.  
10956009 S.Sen, G.Karthikeyan, and B.J.Rao (2000).
RecA realigns suboptimally paired frames of DNA repeats through a process that requires ATP hydrolysis.
  Biochemistry, 39, 10196-10206.  
  10357855 F.Pâques, and J.E.Haber (1999).
Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae.
  Microbiol Mol Biol Rev, 63, 349-404.  
10465767 G.Bertucat, R.Lavery, and C.Prévost (1999).
A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices.
  Biophys J, 77, 1562-1576.  
10390616 J.E.Haber (1999).
DNA recombination: the replication connection.
  Trends Biochem Sci, 24, 271-275.  
10619018 R.C.Gupta, E.Folta-Stogniew, S.O'Malley, M.Takahashi, and C.M.Radding (1999).
Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein.
  Mol Cell, 4, 705-714.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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