spacer
spacer

PDBsum entry 1f1z

Go to PDB code: 
protein metals Protein-protein interface(s) links
DNA binding protein PDB id
1f1z
Jmol
Contents
Protein chains
260 a.a. *
Metals
_CL ×2
_MG ×4
Waters ×292
* Residue conservation analysis
PDB id:
1f1z
Name: DNA binding protein
Title: Tnsa, a catalytic component of the tn7 transposition system
Structure: Tnsa endonuclease. Chain: a, b. Synonym: transposase
Source: Escherichia coli. Organism_taxid: 562. Cell_line: xa90
Resolution:
2.40Å     R-factor:   0.202     R-free:   0.254
Authors: A.B.Hickman,Y.Li,S.V.Mathew,E.W.May,N.L.Craig,F.Dyda
Key ref:
A.B.Hickman et al. (2000). Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol Cell, 5, 1025-1034. PubMed id: 10911996 DOI: 10.1016/S1097-2765(00)80267-1
Date:
21-May-00     Release date:   28-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13988  (TNSA_ECOLX) -  Transposon Tn7 transposition protein TnsA
Seq:
Struc:
273 a.a.
260 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasmic chromosome   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     nucleic acid binding     4 terms  

 

 
DOI no: 10.1016/S1097-2765(00)80267-1 Mol Cell 5:1025-1034 (2000)
PubMed id: 10911996  
 
 
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, F.Dyda.
 
  ABSTRACT  
 
Transposition requires a coordinated series of DNA breakage and joining reactions. The Tn7 transposase contains two proteins: TnsA, which carries out DNA breakage at the 5' ends of the transposon, and TnsB, which carries out breakage and joining at the 3' ends of the transposon. TnsB is a member of the retroviral integrase superfamily whose hallmark is a conserved DDE motif. We report here the structure of TnsA at 2.4 A resolution. Surprisingly, the TnsA fold is that of a type II restriction endonuclease. Thus, Tn7 transposition involves a collaboration between polypeptides, one containing a DDE motif and one that does not. This result indicates that the range of biological processes that utilize restriction enzyme-like folds also includes DNA transposition.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of the Restriction Endonuclease Folds of TnsA, the Vsr Endonuclease, FokI, and Cfr10IThe conserved central β sheet fold is highlighted in green. Only the N-terminal catalytic domains of FokI and TnsA are shown.
Figure 5.
Figure 5. The TnsA Active Site Contains Two Bound Mg^2+ IonsRibbons ([9]) representation of the TnsA active site showing the bound Mg^2+ ions and coordinating ligands. The difference electron density for the Mg^2+ ions (orange) and the anomalous difference density for Cl^− (blue) is contoured at 4σ. The red spheres represent coordinating water molecules, and the connecting lines are hydrogen bonds. V131^O indicates that the coordinating ligand is the main chain carbonyl oxygen.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 5, 1025-1034) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23135398 S.P.Montaño, Y.Z.Pigli, and P.A.Rice (2012).
The Mu transpososome structure sheds light on DDE recombinase evolution.
  Nature, 491, 413-417.
PDB code: 4fcy
21212362 Y.Furuta, M.Kawai, K.Yahara, N.Takahashi, N.Handa, T.Tsuru, K.Oshima, M.Yoshida, T.Azuma, M.Hattori, I.Uchiyama, and I.Kobayashi (2011).
Birth and death of genes linked to chromosomal inversion.
  Proc Natl Acad Sci U S A, 108, 1501-1506.  
20067338 A.B.Hickman, M.Chandler, and F.Dyda (2010).
Integrating prokaryotes and eukaryotes: DNA transposases in light of structure.
  Crit Rev Biochem Mol Biol, 45, 50-69.  
19858101 C.Claeys Bouuaert, and R.Chalmers (2010).
Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage.
  Nucleic Acids Res, 38, 190-202.  
19649713 C.Claeys Bouuaert, and R.M.Chalmers (2010).
Gene therapy vectors: the prospects and potentials of the cut-and-paste transposons.
  Genetica, 138, 473-484.  
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
18694512 J.H.Keith, C.A.Schaeper, T.S.Fraser, and M.J.Fraser (2008).
Mutational analysis of highly conserved aspartate residues essential to the catalytic core of the piggyBac transposase.
  BMC Mol Biol, 9, 73.  
17524420 E.S.Vanamee, J.Berriman, and A.K.Aggarwal (2007).
An EM view of the FokI synaptic complex by single particle analysis.
  J Mol Biol, 370, 207-212.  
17242028 J.Orlowski, M.Boniecki, and J.M.Bujnicki (2007).
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
  Bioinformatics, 23, 527-530.  
17214552 L.Mones, I.Simon, and M.Fuxreiter (2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
  Biol Chem, 388, 73-78.  
16511570 J.M.Richardson, A.Dawson, N.O'Hagan, P.Taylor, D.J.Finnegan, and M.D.Walkinshaw (2006).
Mechanism of Mos1 transposition: insights from structural analysis.
  EMBO J, 25, 1324-1334.
PDB code: 2f7t
15985153 D.J.Rigden (2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
  BMC Struct Biol, 5, 9.  
16308566 E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, and A.K.Aggarwal (2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
  EMBO J, 24, 4198-4208.
PDB codes: 2ezv 2f03
16011798 J.Kosinski, M.Feder, and J.M.Bujnicki (2005).
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
  BMC Bioinformatics, 6, 172.  
15972856 L.N.Kinch, K.Ginalski, L.Rychlewski, and N.V.Grishin (2005).
Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
  Nucleic Acids Res, 33, 3598-3605.  
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
15257292 D.R.Ronning, Y.Li, Z.N.Perez, P.D.Ross, A.B.Hickman, N.L.Craig, and F.Dyda (2004).
The carboxy-terminal portion of TnsC activates the Tn7 transposase through a specific interaction with TnsA.
  EMBO J, 23, 2972-2981.
PDB code: 1t0f
15242409 J.M.Jones, and M.Gellert (2004).
The taming of a transposon: V(D)J recombination and the immune system.
  Immunol Rev, 200, 233-248.  
15562004 M.Saravanan, J.M.Bujnicki, I.A.Cymerman, D.N.Rao, and V.Nagaraja (2004).
Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.
  Nucleic Acids Res, 32, 6129-6135.  
15242410 V.L.Brandt, and D.B.Roth (2004).
V(D)J recombination: how to tame a transposase.
  Immunol Rev, 200, 249-260.  
12535535 A.Dawson, and D.J.Finnegan (2003).
Excision of the Drosophila mariner transposon Mos1. Comparison with bacterial transposition and V(D)J recombination.
  Mol Cell, 11, 225-235.  
12750473 G.Sasnauskas, S.E.Halford, and V.Siksnys (2003).
How the BfiI restriction enzyme uses one active site to cut two DNA strands.
  Proc Natl Acad Sci U S A, 100, 6410-6415.  
12876363 H.Viadiu, E.S.Vanamee, E.M.Jacobson, I.Schildkraut, and A.K.Aggarwal (2003).
Crystallization of restriction endonuclease SfiI in complex with DNA.
  Acta Crystallogr D Biol Crystallogr, 59, 1493-1495.  
12519752 K.L.Carrick, and M.D.Topal (2003).
Amino acid substitutions at position 43 of NaeI endonuclease. Evidence for changes in NaeI structure.
  J Biol Chem, 278, 9733-9739.  
14682279 M.J.Curcio, and K.M.Derbyshire (2003).
The outs and ins of transposition: from mu to kangaroo.
  Nat Rev Mol Cell Biol, 4, 865-877.  
14576294 M.Mucke, D.H.Kruger, and M.Reuter (2003).
Diversity of type II restriction endonucleases that require two DNA recognition sites.
  Nucleic Acids Res, 31, 6079-6084.  
12655005 N.K.Raghavendra, and D.N.Rao (2003).
Functional cooperation between exonucleases and endonucleases--basis for the evolution of restriction enzymes.
  Nucleic Acids Res, 31, 1888-1896.  
12753185 Y.Tourand, K.Kobryn, and G.Chaconas (2003).
Sequence-specific recognition but position-dependent cleavage of two distinct telomeres by the Borrelia burgdorferi telomere resolvase, ResT.
  Mol Microbiol, 48, 901-911.  
14592987 Z.Skelding, J.Queen-Baker, and N.L.Craig (2003).
Alternative interactions between the Tn7 transposase and the Tn7 target DNA binding protein regulate target immunity and transposition.
  EMBO J, 22, 5904-5917.  
11818524 J.Bitinaite, and I.Schildkraut (2002).
Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease.
  Proc Natl Acad Sci U S A, 99, 1164-1169.  
12093751 J.M.Hadden, A.C.Déclais, S.E.Phillips, and D.M.Lilley (2002).
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
  EMBO J, 21, 3505-3515.
PDB codes: 1m0d 1m0i
12356742 M.Mücke, G.Grelle, J.Behlke, R.Kraft, D.H.Krüger, and M.Reuter (2002).
EcoRII: a restriction enzyme evolving recombination functions?
  EMBO J, 21, 5262-5268.  
12093750 Z.Skelding, R.Sarnovsky, and N.L.Craig (2002).
Formation of a nucleoprotein complex containing Tn7 and its target DNA regulates transposition initiation.
  EMBO J, 21, 3494-3504.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11557807 I.Kobayashi (2001).
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
  Nucleic Acids Res, 29, 3742-3756.  
11387225 N.P.Tavakoli, and K.M.Derbyshire (2001).
Tipping the balance between replicative and simple transposition.
  EMBO J, 20, 2923-2930.  
11359901 W.Li, F.C.Chang, and S.Desiderio (2001).
Rag-1 mutations associated with B-cell-negative scid dissociate the nicking and transesterification steps of V(D)J recombination.
  Mol Cell Biol, 21, 3935-3946.  
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.