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protein dna_rna Protein-protein interface(s) links
DNA binding protein/DNA PDB id
1gdt
Jmol
Contents
Protein chains
183 a.a. *
DNA/RNA
Waters ×29
* Residue conservation analysis
PDB id:
1gdt
Name: DNA binding protein/DNA
Title: Crystal structure of a site-specific recombinase, gamma- delta resolvase complexed with a 34 bp cleavage site
Structure: Site i of res DNA. Chain: c. Synonym: crossover site or cleavage site. Engineered: yes. Site i of res DNA. Chain: d, f. Synonym: crossover site or cleavage site. Engineered: yes. Site i of res DNA.
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Strain: strains that contain f episome. Gene: tnpr. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
3.00Å     R-factor:   0.235    
Authors: W.Yang,T.A.Steitz
Key ref: 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. PubMed id: 7628011 DOI: 10.1016/0092-8674(95)90307-0
Date:
11-Apr-95     Release date:   03-Apr-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription   3 terms 
  Biochemical function     recombinase activity     2 terms  

 

 
DOI no: 10.1016/0092-8674(95)90307-0 Cell 82:193-207 (1995)
PubMed id: 7628011  
 
 
Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
W.Yang, T.A.Steitz.
 
  ABSTRACT  
 
The structure of gamma delta resolvase complexed with a 34 bp substrate DNA has been determined at 3.0 A resolution. The DNA is sharply bent by 60 degrees toward the major groove and away from the resolvase catalytic domains at the recombination crossover point. The C-terminal one third of resolvase, which was disordered in the absence of DNA, forms an arm and a 3-helix DNA-binding domain on the opposite side of the DNA from the N-terminal domain. The arms wrap around the minor groove of the central 16 bp, and the DNA-binding domains interact with the major grooves near the outer boundaries of the binding site. The resolvase dimer is asymmetric, particularly in the arm region, implying a conformational adaptability that may be important for resolvase binding to different DNA sites in the synaptosome. It also raises the possibility of a sequential single-strand cleavage mechanism.
 

Literature references that cite this PDB file's key reference

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21087076 W.Yang (2010).
Topoisomerases and site-specific recombinases: similarities in structure and mechanism.
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19282480 R.M.Gordley, C.A.Gersbach, and C.F.Barbas (2009).
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15454079 G.Dhar, E.R.Sanders, and R.C.Johnson (2004).
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Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation.
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15469828 M.Nöllmann, J.He, O.Byron, and W.M.Stark (2004).
Solution structure of the Tn3 resolvase-crossover site synaptic complex.
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15306021 V.Adams, I.S.Lucet, D.Lyras, and J.I.Rood (2004).
DNA binding properties of TnpX indicate that different synapses are formed in the excision and integration of the Tn4451 family.
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Chimeric recombinases with designed DNA sequence recognition.
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The architecture of the gammadelta resolvase crossover site synaptic complex revealed by using constrained DNA substrates.
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11972771 M.C.Smith, and H.M.Thorpe (2002).
Diversity in the serine recombinases.
  Mol Microbiol, 44, 299-307.  
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Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting.
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Testing water-mediated DNA recognition by the Hin recombinase.
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Sex-specific gene regulation. The Doublesex DM motif is a bipartite DNA-binding domain.
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Directed evolution of a recombinase for improved genomic integration at a native human sequence.
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A model for the gamma delta resolvase synaptic complex.
  Mol Cell, 8, 623-631.  
11114897 O.Z.Nanassy, and K.T.Hughes (2001).
Hin recombinase mutants functionally disrupted in interactions with Fis.
  J Bacteriol, 183, 28-35.  
11069650 H.M.Thorpe, S.E.Wilson, and M.C.Smith (2000).
Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31.
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Structural and thermodynamic strategies for site-specific DNA binding proteins.
  Structure, 8, 1015-1023.  
  10898790 L.Zhu, J.Wilken, N.B.Phillips, U.Narendra, G.Chan, S.M.Stratton, S.B.Kent, and M.A.Weiss (2000).
Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers.
  Genes Dev, 14, 1750-1764.
PDB code: 1lpv
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
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Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination.
  Mol Cell, 4, 949-959.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
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Predicting conformational switches in proteins.
  Protein Sci, 8, 1752-1764.  
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.  
  10585967 P.Hindmarsh, and J.Leis (1999).
Retroviral DNA integration.
  Microbiol Mol Biol Rev, 63, 836.  
10476039 S.Minakhina, G.Kholodii, S.Mindlin, O.Yurieva, and V.Nikiforov (1999).
Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases.
  Mol Microbiol, 33, 1059-1068.  
10690407 T.Komano (1999).
Shufflons: multiple inversion systems and integrons.
  Annu Rev Genet, 33, 171-191.  
9663657 C.C.Liu, R.Hühne, J.Tu, E.Lorbach, and P.Dröge (1998).
The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases.
  Genes Cells, 3, 221-233.  
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The role of supercoiling in mycobacteriophage L5 integrative recombination.
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9600906 D.M.Tanenbaum, Y.Wang, S.P.Williams, and P.B.Sigler (1998).
Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains.
  Proc Natl Acad Sci U S A, 95, 5998-6003.
PDB code: 1a52
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.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
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.  
9722507 M.Hartung, and B.Kisters-Woike (1998).
Cre mutants with altered DNA binding properties.
  J Biol Chem, 273, 22884-22891.  
9774480 M.Lehmann, T.Siegmund, K.G.Lintermann, and G.Korge (1998).
The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain.
  J Biol Chem, 273, 28504-28509.  
  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.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
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Crystal structure of the signal sequence binding subunit of the signal recognition particle.
  Cell, 94, 181-191.
PDB code: 2ffh
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Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion.
  Genes Dev, 12, 2803-2816.  
9759484 S.Verma, and F.Eckstein (1998).
Modified oligonucleotides: synthesis and strategy for users.
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Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex.
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Solving the cis/trans paradox in the Int family of recombinases.
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Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements.
  FEMS Microbiol Rev, 21, 157-178.  
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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.  
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
9214634 K.Myung, D.M.He, S.E.Lee, and E.A.Hendrickson (1997).
KARP-1: a novel leucine zipper protein expressed from the Ku86 autoantigen locus is implicated in the control of DNA-dependent protein kinase activity.
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Lac repressor-operator complex.
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Solution structure of the N-terminal zinc binding domain of HIV-1 integrase.
  Nat Struct Biol, 4, 567-577.
PDB codes: 1wja 1wjb 1wjc 1wjd
9368738 N.D.Grindley (1997).
Site-specific recombination: synapsis and strand exchange revealed.
  Curr Biol, 7, R608-R612.  
9242914 N.L.Craig (1997).
Target site selection in transposition.
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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.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
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Site-specific recombination in plane view.
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The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis.
  Cell, 85, 257-269.  
8913682 H.S.Pappa, A.E.Stewart, and N.Q.McDonald (1996).
Incorporating anomalous scattering centres into macromolecules.
  Curr Opin Struct Biol, 6, 611-616.  
8612279 H.Savilahti, and K.Mizuuchi (1996).
Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase.
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8759784 J.C.Alonso, S.Ayora, I.Canosa, F.Weise, and F.Rojo (1996).
Site-specific recombination in gram-positive theta-replicating plasmids.
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Retroviral integrase, putting the pieces together.
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The Hin dimer interface is critical for Fis-mediated activation of the catalytic steps of site-specific DNA inversion.
  Curr Biol, 6, 163-177.  
8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
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  8599941 Z.Wang, and P.Dröge (1996).
Differential control of transcription-induced and overall DNA supercoiling by eukaryotic topoisomerases in vitro.
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7606780 K.M.Reinisch, L.Chen, G.L.Verdine, and W.N.Lipscomb (1995).
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
  Cell, 82, 143-153.
PDB code: 1dct
8548278 M.Oram, M.D.Szczelkun, and S.E.Halford (1995).
Recombination. Pieces of the site-specific recombination puzzle.
  Curr Biol, 5, 1106-1109.  
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Catalytic residues of gamma delta resolvase act in cis.
  EMBO J, 14, 5129-5140.  
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DNA transposition: from a black box to a color monitor.
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Resolving a resolvase.
  Nat Struct Biol, 2, 607-609.  
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