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Site-specific recombinase PDB id
2rsl
Jmol
Contents
Protein chains
115 a.a. *
120 a.a. *
Ligands
SO4 ×3
Waters ×165
* Residue conservation analysis
PDB id:
2rsl
Name: Site-specific recombinase
Title: Refinement of gamma delta resolvase reveals a strikingly flexible molecule
Structure: Gamma delta-resolvase. Chain: a, b, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
2.30Å     R-factor:   0.200    
Authors: P.A.Rice,T.A.Steitz
Key ref:
P.A.Rice and T.A.Steitz (1994). Refinement of gamma delta resolvase reveals a strikingly flexible molecule. Structure, 2, 371-384. PubMed id: 8081753 DOI: 10.1016/S0969-2126(00)00039-3
Date:
08-Sep-93     Release date:   30-Apr-94    
Supersedes: 1rsl
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03012  (TNR1_ECOLI) -  Transposon gamma-delta resolvase
Seq:
Struc: 		183 a.a.
115 a.a.
Protein chains
Pfam   ArchSchema ?
P03012  (TNR1_ECOLI) -  Transposon gamma-delta resolvase
Seq:
Struc: 		183 a.a.
120 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA recombination   1 term 
  Biochemical function     recombinase activity     2 terms  

 

 
DOI no: 10.1016/S0969-2126(00)00039-3 Structure 2:371-384 (1994)
PubMed id: 8081753  
 
 
Refinement of gamma delta resolvase reveals a strikingly flexible molecule.
P.A.Rice, T.A.Steitz.
 
  ABSTRACT  
 
BACKGROUND: gamma delta resolvase is a 20.5 kDa enzyme that catalyzes a site-specific recombination in the second step of the transposition of the gamma delta transposon and requires no cofactors other than Mg2+ for activity. Dimers of resolvase bind cooperatively to DNA at three inverted repeat sequences of differing geometry but catalyze recombination at only one site. RESULTS: The structure of the catalytic domain of gamma delta resolvase, which provides the protein-protein interactions in the synaptic complex, has been refined to an R-factor of 20% at 2.3 A resolution. The structures of the three independent monomers in the asymmetric unit are similar but not identical. Differences occur in the positions of surface loops and in the overall twist of the central beta-sheet of the molecule. The crystal also gives two independent structures for the dimeric form of the molecule, which also show significant differences in the relative orientations of their subunits. CONCLUSION: Resolvase is an unusually flexible protein. This conformational adaptability may be necessary to allow each of the 12 resolvase subunits in the synaptic complex to play a different but specific role in wrapping DNA, binding sites of differing geometry and catalyzing recombination.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Superpositions of monomers 1 and 2 (stereo view). (a) Monomer 1 (blue) is shown superimposed on monomer 2 (green) by a least squares procedure using the α-carbons of helices A and B as guides. Due to a difference in the overall twist of the central β -sheet, the superposition becomes increasingly poor towards the carboxy-terminal portion of the molecule. (The extra long Cα–Cα bond in monomer 1 is between residues 37 and 45, as the turn consisting of residues 38–44 is disordered in this monomer.) (b) Monomer 1 superimposed on monomer 2 using the α-carbons of helices D and E as guides. This placement of monomer 1 differs from the one in part (a) by a rotation of 10.5°. Figure 8. Superpositions of monomers 1 and 2 (stereo view). (a) Monomer 1 (blue) is shown superimposed on monomer 2 (green) by a least squares procedure using the α-carbons of helices A and B as guides. Due to a difference in the overall twist of the central β -sheet, the superposition becomes increasingly poor towards the carboxy-terminal portion of the molecule. (The extra long Cα–Cα bond in monomer 1 is between residues 37 and 45, as the turn consisting of residues 38–44 is disordered in this monomer.) (b) Monomer 1 superimposed on monomer 2 using the α-carbons of helices D and E as guides. This placement of monomer 1 differs from the one in part (a) by a rotation of 10.5°.
Figure 13.
Figure 13. A packing defect inside the hydrophobic core. The structure of the cavity inside monomer 3, as defined using a 1.2 å probe radius (see text) and those side chains which form its boundaries are shown. A very similar cavity is found in monomer 2, and a similar but slightly larger and more elongated cavity is found in monomer 1. Figure 13. A packing defect inside the hydrophobic core. The structure of the cavity inside monomer 3, as defined using a 1.2 å probe radius (see text) and those side chains which form its boundaries are shown. A very similar cavity is found in monomer 2, and a similar but slightly larger and more elongated cavity is found in monomer 1. (Figure prepared using FRODO [[3]47].)
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 371-384) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
18439894 K.W.Mouw, S.J.Rowland, M.M.Gajjar, M.R.Boocock, W.M.Stark, and P.A.Rice (2008).
Architecture of a serine recombinase-DNA regulatory complex.
  Mol Cell, 30, 145-155.
PDB code: 2r0q
16740123 A.Bhardwaj, K.Welfle, R.Misselwitz, S.Ayora, J.C.Alonso, and H.Welfle (2006).
Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific beta recombinase, and identification of a folding intermediate.
  Biol Chem, 387, 525-533.  
15980165 M.Nöllmann, O.Byron, and W.M.Stark (2005).
Behavior of Tn3 resolvase in solution and its interaction with res.
  Biophys J, 89, 1920-1931.  
15994378 W.Li, S.Kamtekar, Y.Xiong, G.J.Sarkis, N.D.Grindley, and T.A.Steitz (2005).
Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.
  Science, 309, 1210-1215.
PDB codes: 1zr2 1zr4
15454079 G.Dhar, E.R.Sanders, and R.C.Johnson (2004).
Architecture of the hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands.
  Cell, 119, 33-45.  
15557256 G.Fuentes, A.Ballesteros, and C.S.Verma (2004).
Specificity in lipases: a computational study of transesterification of sucrose.
  Protein Sci, 13, 3092-3103.  
14763971 M.E.Burke, P.H.Arnold, J.He, S.V.Wenwieser, S.J.Rowland, M.R.Boocock, and W.M.Stark (2004).
Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation.
  Mol Microbiol, 51, 937-948.  
15469828 M.Nöllmann, J.He, O.Byron, and W.M.Stark (2004).
Solution structure of the Tn3 resolvase-crossover site synaptic complex.
  Mol Cell, 16, 127-137.  
  14527421 A.E.Leschziner, and N.D.Grindley (2003).
The architecture of the gammadelta resolvase crossover site synaptic complex revealed by using constrained DNA substrates.
  Mol Cell, 12, 775-781.  
  11583624 G.J.Sarkis, L.L.Murley, A.E.Leschziner, M.R.Boocock, W.M.Stark, and N.D.Grindley (2001).
A model for the gamma delta resolvase synaptic complex.
  Mol Cell, 8, 623-631.  
10413462 J.Greenwald, V.Le, S.L.Butler, F.D.Bushman, and S.Choe (1999).
The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
  Biochemistry, 38, 8892-8898.
PDB codes: 1b92 1b9d 1b9f
10064606 P.H.Arnold, D.G.Blake, N.D.Grindley, M.R.Boocock, and W.M.Stark (1999).
Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity.
  EMBO J, 18, 1407-1414.  
  9827807 L.L.Murley, and N.D.Grindley (1998).
Architecture of the gamma delta resolvase synaptosome: oriented heterodimers identity interactions essential for synapsis and recombination.
  Cell, 95, 553-562.  
  9732277 S.K.Merickel, M.J.Haykinson, and R.C.Johnson (1998).
Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion.
  Genes Dev, 12, 2803-2816.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9348666 B.Hallet, and D.J.Sherratt (1997).
Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements.
  FEMS Microbiol Rev, 21, 157-178.  
9082984 H.J.Kwon, R.Tirumalai, A.Landy, and T.Ellenberger (1997).
Flexibility in DNA recombination: structure of the lambda integrase catalytic core.
  Science, 276, 126-131.
PDB code: 1ae9
  9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
9336450 P.J.Artymiuk, T.A.Ceska, D.Suck, and J.R.Sayers (1997).
Prokaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.
  Nucleic Acids Res, 25, 4224-4229.  
  8612279 H.Savilahti, and K.Mizuuchi (1996).
Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase.
  Cell, 85, 271-280.  
  8673463 M.J.Haykinson, L.M.Johnson, J.Soong, and R.C.Johnson (1996).
The Hin dimer interface is critical for Fis-mediated activation of the catalytic steps of site-specific DNA inversion.
  Curr Biol, 6, 163-177.  
7596288 A.E.Leschziner, M.R.Boocock, and N.D.Grindley (1995).
The tyrosine-6 hydroxyl of gamma delta resolvase is not required for the DNA cleavage and rejoining reactions.
  Mol Microbiol, 15, 865-870.  
7552718 R.Craigie (1995).
Resolving a resolvase.
  Nat Struct Biol, 2, 607-609.  
  7628011 W.Yang, and T.A.Steitz (1995).
Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
  Cell, 82, 193-207.
PDB code: 1gdt
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 code is shown on the right.