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Recombination/DNA PDB id
2r0q
Jmol
Contents
Protein chains
193 a.a. *
DNA/RNA
Ligands
SO4 ×2
* Residue conservation analysis
PDB id:
2r0q
Name: Recombination/DNA
Title: Crystal structure of a serine recombinase- DNA regulatory complex
Structure: Putative transposon tn552 DNA-invertase bin3. Chain: c, d, e, f. Engineered: yes. 31-mer. Chain: a, g. Engineered: yes. Other_details: site ii DNA strand 1. 31-mer. Chain: b, h.
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: nctc 9789. Gene: bin3. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Resolution:
3.20Å     R-factor:   0.267     R-free:   0.291
Authors: P.A.Rice,K.W.Mouw
Key ref:
K.W.Mouw et al. (2008). Architecture of a serine recombinase-DNA regulatory complex. Mol Cell, 30, 145-155. PubMed id: 18439894 DOI: 10.1016/j.molcel.2008.02.023
Date:
21-Aug-07     Release date:   01-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P20384  (BIN3_STAAU) -  Putative transposon Tn552 DNA-invertase bin3
Seq:
Struc: 		202 a.a.
193 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transposition   4 terms 
  Biochemical function     recombinase activity     2 terms  

 

 
DOI no: 10.1016/j.molcel.2008.02.023 Mol Cell 30:145-155 (2008)
PubMed id: 18439894  
 
 
Architecture of a serine recombinase-DNA regulatory complex.
K.W.Mouw, S.J.Rowland, M.M.Gajjar, M.R.Boocock, W.M.Stark, P.A.Rice.
 
  ABSTRACT  
 
An essential feature of many site-specific recombination systems is their ability to regulate the direction and topology of recombination. Resolvases from the serine recombinase family assemble an interwound synaptic complex that harnesses negative supercoiling to drive the forward reaction and promote recombination between properly oriented sites. To better understand the interplay of catalytic and regulatory functions within these synaptic complexes, we have solved the structure of the regulatory site synapse in the Sin resolvase system. It reveals an unexpected synaptic interface between helix-turn-helix DNA-binding domains that is also highlighted in a screen for synapsis mutants. The tetramer defined by this interface provides the foundation for a robust model of the synaptic complex, assembled entirely from available crystal structures, that gives insight into how the catalytic activity of Sin and other serine recombinases may be regulated.
 
  Selected figure(s)  
 
Figure 3.
Tetrameric Interfaces Observed in the Crystal Structure (A) An interface involving the N-terminal catalytic domains places the bound site II duplexes along the outside of the complex. The duplexes define a right-handed ( +) node crossing; this structure is thus a poor candidate for the site II synaptic complex. (B) The interface between DNA-binding domains defines a tetramer in which the bound duplexes are near the center of the complex and cross to form a left-handed ([minus sign]) node. The orientation and close proximity of the duplexes make this a good candidate for the site II synaptic interface. (C) A close-up view of the interdigitating interaction involving the side chains of residues F52 and R54 from two adjacent dimer complexes in the crystal structure (see also Figure S1). Mol Cell. 2008 April 25; 30(2): 145–155. doi: 10.1016/j.molcel.2008.02.023. Copyright [copyright] 2008 ELL & Excerpta Medica
Figure 4.
Stereo View of the Interface between Sin DNA-Binding Domains in the Site II Synaptic Tetramer Residues from helix F comprise much of the interface. Side chains are shown for all residues that, when mutated, confer a defect in synapsis and recombination (see Figure 5 Figure 5-). Red, V163 and I164; orange, Q160, K161, and R167; yellow, E170 and N186; and magenta, S153. Also shown is H166 (cyan), the position of the suppressor mutation H166R. The DNA-binding domains of Sin subunits bound at site IIL (green) and site IIR (blue) are shown (N-terminal domains not shown). Mol Cell. 2008 April 25; 30(2): 145–155. doi: 10.1016/j.molcel.2008.02.023. Copyright [copyright] 2008 ELL & Excerpta Medica
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2008, 30, 145-155) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21303688 Q.Song, T.Ye, and X.Zhang (2011).
Proteins responsible for lysogeny of deep-sea thermophilic bacteriophage GVE2 at high temperature.
  Gene, 479, 1-9.  
21428950 W.Marshall Stark, M.R.Boocock, F.J.Olorunniji, and S.J.Rowland (2011).
Intermediates in serine recombinase-mediated site-specific recombination.
  Biochem Soc Trans, 39, 617-622.  
20972794 Y.Wang, Y.Y.Yau, D.Perkins-Balding, and J.G.Thomson (2011).
Recombinase technology: applications and possibilities.
  Plant Cell Rep, 30, 267-285.  
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
19396172 F.F.Yin, S.Bailey, C.A.Innis, M.Ciubotaru, S.Kamtekar, T.A.Steitz, and D.G.Schatz (2009).
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.
  Nat Struct Mol Biol, 16, 499-508.
PDB codes: 3gna 3gnb
19789272 F.J.Olorunniji, and W.M.Stark (2009).
The catalytic residues of Tn3 resolvase.
  Nucleic Acids Res, 37, 7590-7602.  
19515933 G.Dhar, M.M.McLean, J.K.Heiss, and R.C.Johnson (2009).
The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands.
  Nucleic Acids Res, 37, 4743-4756.  
18704739 J.G.Thomson, Y.Y.Yau, R.Blanvillain, D.Chiniquy, R.Thilmony, and D.W.Ow (2009).
ParA resolvase catalyzes site-specific excision of DNA from the Arabidopsis genome.
  Transgenic Res, 18, 237-248.  
19788335 J.L.Gilmore, Y.Suzuki, G.Tamulaitis, V.Siksnys, K.Takeyasu, and Y.L.Lyubchenko (2009).
Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy.
  Biochemistry, 48, 10492-10498.  
19766564 J.M.Richardson, S.D.Colloms, D.J.Finnegan, and M.D.Walkinshaw (2009).
Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote.
  Cell, 138, 1096-1108.
PDB codes: 3hos 3hot
19508283 S.J.Rowland, M.R.Boocock, A.L.McPherson, K.W.Mouw, P.A.Rice, and W.M.Stark (2009).
Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.
  Mol Microbiol, 74, 282-298.  
19015124 F.J.Olorunniji, J.He, S.V.Wenwieser, M.R.Boocock, and W.M.Stark (2008).
Synapsis and catalysis by activated Tn3 resolvase mutants.
  Nucleic Acids Res, 36, 7181-7191.  
18462666 R.C.Johnson, and J.K.Heiss (2008).
Assembly of a tightly interwound DNA recombination complex poised for deletion.
  Structure, 16, 653-655.  
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.