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Site-specific recombinase PDB id
1gdr
Jmol
Contents
Protein chain
105 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
1gdr
Name: Site-specific recombinase
Title: Model for a DNA mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits
Structure: Gamma delta-resolvase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Resolution:
3.50Å     R-factor:   0.310    
Authors: P.A.Rice,T.A.Steitz
Key ref: P.A.Rice and T.A.Steitz (1994). Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits. Embo J, 13, 1514-1524. PubMed id: 8156989 Ref: Full text
Date:
31-Aug-93     Release date:   30-Apr-94    
 Headers
 References

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

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

 

 
    Key reference    
 
 
Full text Embo J 13:1514-1524 (1994)
PubMed id: 8156989  
 
 
Model for a DNA-mediated synaptic complex suggested by crystal packing of gamma delta resolvase subunits.
P.A.Rice, T.A.Steitz.
 
  ABSTRACT  
 
The packing arrangement of the 12 subunits of intact gamma delta resolvase in the unit cell of a hexagonal crystal form suggests a model for site-specific recombination that involves a DNA-mediated synaptic intermediate. The crystal structure has been determined by molecular replacement and partially refined at 2.8/3.5 A resolution. Although the small DNA-binding domain is disordered in these crystals, packing considerations show that only a small region of space in the crystal could accommodate a domain of its size. A family of related models for a synaptic complex between two DNA duplexes and 12 monomers that are arranged as situated in the crystal is consistent with the known topology of the complex and the distances between the three resolvase dimer-binding sites per DNA; further, these models place the two DNA recombination sites in contact with each other between two resolvase dimers, implying that strand exchange is accomplished through direct DNA-DNA interaction. A major role postulated, then, for the resolvase protein assembly is to stabilize a res DNA structure that is close to the topological transition state of the reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
  Crit Rev Biochem Mol Biol, 45, 520-534.  
19789272 F.J.Olorunniji, and W.M.Stark (2009).
The catalytic residues of Tn3 resolvase.
  Nucleic Acids Res, 37, 7590-7602.  
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.  
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
18682229 P.Yuan, K.Gupta, and G.D.Van Duyne (2008).
Tetrameric structure of a serine integrase catalytic domain.
  Structure, 16, 1275-1286.
PDB code: 3bvp
16756503 N.D.Grindley, K.L.Whiteson, and P.A.Rice (2006).
Mechanisms of site-specific recombination.
  Annu Rev Biochem, 75, 567-605.  
16807292 S.Kamtekar, R.S.Ho, M.J.Cocco, W.Li, S.V.Wenwieser, M.R.Boocock, N.D.Grindley, and T.A.Steitz (2006).
Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.
  Proc Natl Acad Sci U S A, 103, 10642-10647.
PDB codes: 2gm4 2gm5
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.  
16077726 P.A.Rice (2005).
Resolving integral questions in site-specific recombination.
  Nat Struct Mol Biol, 12, 641-643.  
15813731 S.J.Rowland, M.R.Boocock, and W.M.Stark (2005).
Regulation of Sin recombinase by accessory proteins.
  Mol Microbiol, 56, 371-382.  
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
15939020 Y.Ma, J.Dostie, G.Dreyfuss, and G.D.Van Duyne (2005).
The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure.
  Structure, 13, 883-892.
PDB code: 1y96
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.  
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.  
14763986 S.K.Merickel, and R.C.Johnson (2004).
Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro.
  Mol Microbiol, 51, 1143-1154.  
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.  
12560501 I.Canosa, G.López, F.Rojo, M.R.Boocock, and J.C.Alonso (2003).
Synapsis and strand exchange in the resolution and DNA inversion reactions catalysed by the beta recombinase.
  Nucleic Acids Res, 31, 1038-1044.  
11994145 S.J.Rowland, W.M.Stark, and M.R.Boocock (2002).
Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting.
  Mol Microbiol, 44, 607-619.  
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.  
10064578 H.K.Song, S.H.Sohn, and S.W.Suh (1999).
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
  EMBO J, 18, 1104-1113.
PDB codes: 1b49 1b5d 1b5e
10449417 N.Sträter, D.J.Sherratt, and S.D.Colloms (1999).
X-ray structure of aminopeptidase A from Escherichia coli and a model for the nucleoprotein complex in Xer site-specific recombination.
  EMBO J, 18, 4513-4522.
PDB code: 1gyt
9576912 H.M.Thorpe, and M.C.Smith (1998).
In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family.
  Proc Natl Acad Sci U S A, 95, 5505-5510.  
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.  
  9691026 O.Z.Nanassy, and K.T.Hughes (1998).
In vivo identification of intermediate stages of the DNA inversion reaction catalyzed by the Salmonella Hin recombinase.
  Genetics, 149, 1649-1663.  
  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.  
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.  
  9194184 B.Pan, Z.Deng, D.Liu, S.Ghosh, and G.P.Mullen (1997).
Secondary and tertiary structural changes in gamma delta resolvase: comparison of the wild-type enzyme, the I110R mutant, and the C-terminal DNA binding domain in solution.
  Protein Sci, 6, 1237-1247.  
9218487 H.M.Lim, H.J.Lee, C.Jaxel, and M.Nadal (1997).
Hin-mediated inversion on positively supercoiled DNA.
  J Biol Chem, 272, 18434-18439.  
9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
  Curr Opin Struct Biol, 7, 76-85.  
  7744017 L.K.Arciszewska, and D.J.Sherratt (1995).
Xer site-specific recombination in vitro.
  EMBO J, 14, 2112-2120.  
7493962 M.D.Andrake, and A.M.Skalka (1995).
Multimerization determinants reside in both the catalytic core and C terminus of avian sarcoma virus integrase.
  J Biol Chem, 270, 29299-29306.  
8548278 M.Oram, M.D.Szczelkun, and S.E.Halford (1995).
Recombination. Pieces of the site-specific recombination puzzle.
  Curr Biol, 5, 1106-1109.  
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
  8081753 P.A.Rice, and T.A.Steitz (1994).
Refinement of gamma delta resolvase reveals a strikingly flexible molecule.
  Structure, 2, 371-384.
PDB code: 2rsl
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.