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PDBsum entry 2bw3
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protein Protein-protein interface(s) links
DNA recombination PDB id
2bw3

 

 

 

 

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Contents
Protein chains
518 a.a. *
84 a.a. *
Waters ×416
* Residue conservation analysis
PDB id:
2bw3
Name: DNA recombination
Title: Three-dimensional structure of the hermes DNA transposase
Structure: Transposase. Chain: a. Engineered: yes. Mutation: yes. Transposase. Chain: b. Engineered: yes
Source: Musca domestica. House fly. Organism_taxid: 7370. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.185     R-free:   0.211
Authors: A.B.Hickman,Z.N.Perez,L.Zhou,P.Musingarimi,R.Ghirlando,J.E.Hinshaw, N.L.Craig,F.Dyda
Key ref:
A.B.Hickman et al. (2005). Molecular architecture of a eukaryotic DNA transposase. Nat Struct Mol Biol, 12, 715-721. PubMed id: 16041385 DOI: 10.1038/nsmb970
Date:
11-Jul-05     Release date:   28-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q25438  (Q25438_MUSDO) -  Hermes transposase from Musca domestica
Seq:
Struc: 		 
Seq:
Struc: 		612 a.a.
518 a.a.*
Protein chain
Pfam   ArchSchema ?
Q25442  (Q25442_MUSDO) -  Transposase from Musca domestica
Seq:
Struc: 		 
Seq:
Struc: 		612 a.a.
84 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 

 
DOI no: 10.1038/nsmb970 Nat Struct Mol Biol 12:715-721 (2005)
PubMed id: 16041385  
 
 
Molecular architecture of a eukaryotic DNA transposase.
A.B.Hickman, Z.N.Perez, L.Zhou, P.Musingarimi, R.Ghirlando, J.E.Hinshaw, N.L.Craig, F.Dyda.
 
  ABSTRACT  
 
Mobile elements and their inactive remnants account for large proportions of most eukaryotic genomes, where they have had central roles in genome evolution. Over 50 years ago, McClintock reported a form of stress-induced genome instability in maize in which discrete DNA segments move between chromosomal locations. Our current mechanistic understanding of enzymes catalyzing transposition is largely limited to prokaryotic transposases. The Hermes transposon from the housefly is part of the eukaryotic hAT superfamily that includes hobo from Drosophila, McClintock's maize Activator and Tam3 from snapdragon. We report here the three-dimensional structure of a functionally active form of the transposase from Hermes at 2.1-A resolution. The Hermes protein has some structural features of prokaryotic transposases, including a domain with a retroviral integrase fold. However, this domain is disrupted by the insertion of an additional domain. Finally, transposition is observed only when Hermes assembles into a hexamer.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of Hermes[79 -612]. (a) Three-domain organization of Hermes[79 -612]. Residues that comprise the DDE motif and Trp319 converge at the active site. The dashed line indicates a disordered region. (b) Close-up of the active site. (c) Plasmid cleavage assay of wild-type (WT) and W319A mutant Hermes[79 -612], visualized on a 1% agarose gel. R-DSB, right-end double-stand break; L-DSB, right-end double-stand break. (d) Target-joining assay using 40-nucleotide, precleaved Hermes left end. SEJ, single-end join; DEJ, double-end join. (e) The hAT dimerization domain (green) winds through the inserted domain and forms the C-terminal portion of the retroviral integrase RNase-like domain. 		Figure 3.
Figure 3. The hexameric form of Hermes[79 -612]. (a) A model for the hexamer was generated using the symmetry elements of the heterotetramer. A noncrystallographic two-fold axis relates the N-terminal domains, and a crystallographic two-fold axis relates the Hermes[79 -612] monomers. The numbers refer to three interfaces, where interfaces 1 and 2 are observed and interface 3 is modeled. (b) Modeled hexamer showing alternating interfaces 2 and 3. Six arrows indicate active sites where Asp180, Asp248 and Glu572 converge (carboxylate oxygen atoms are shown in red). (c) Gallery of electron micrographs of negatively stained active Hermes[79 -612]. Scale bar, 20 nm. (d) Surface representation of Hermes[79 -612] showing one possible mode of DNA binding (DNA is shown as ball-and-stick model and Hermes[79 -162] as ribbons).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 715-721) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21356525 Q.Meng, K.Chen, L.Ma, S.Hu, and J.Yu (2011).
A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases.
  J Genet Genomics, 38, 63-70.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21518873 Y.W.Yuan, and S.R.Wessler (2011).
The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies.
  Proc Natl Acad Sci U S A, 108, 7884-7889.  
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.  
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.  
20615441 I.V.Nesmelova, and P.B.Hackett (2010).
DDE transposases: Structural similarity and diversity.
  Adv Drug Deliv Rev, 62, 1187-1195.  
20339871 M.Deprá, Y.Panzera, A.Ludwig, V.L.Valente, and E.L.Loreto (2010).
Hosimary: a new hAT transposon group involved in horizontal transfer.
  Mol Genet Genomics, 283, 451-459.  
20004590 S.D.Fugmann (2010).
The origins of the Rag genes--from transposition to V(D)J recombination.
  Semin Immunol, 22, 10-16.  
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
19647518 G.J.Grundy, S.Ramón-Maiques, E.K.Dimitriadis, S.Kotova, C.Biertümpfel, J.B.Heymann, A.C.Steven, M.Gellert, and W.Yang (2009).
Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex.
  Mol Cell, 35, 217-227.  
19720743 J.Bischerour, C.Lu, D.B.Roth, and R.Chalmers (2009).
Base flipping in V(D)J recombination: insights into the mechanism of hairpin formation, the 12/23 rule, and the coordination of double-strand breaks.
  Mol Cell Biol, 29, 5889-5899.  
19593448 J.Bischerour, and R.Chalmers (2009).
Base flipping in tn10 transposition: an active flip and capture mechanism.
  PLoS One, 4, e6201.  
19436716 J.L.Gordon, K.P.Byrne, and K.H.Wolfe (2009).
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.
  PLoS Genet, 5, e1000485.  
19500590 L.M.Gwyn, M.M.Peak, P.De, N.S.Rahman, and K.K.Rodgers (2009).
A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity.
  J Mol Biol, 390, 863-878.  
19165139 M.Nowotny (2009).
Retroviral integrase superfamily: the structural perspective.
  EMBO Rep, 10, 144-151.  
18340538 M.de Freitas Ortiz, and E.L.Loreto (2009).
Characterization of new hAT transposable elements in 12 Drosophila genomes.
  Genetica, 135, 67-75.  
19366812 R.A.Subramanian, L.A.Cathcart, E.S.Krafsur, P.W.Atkinson, and D.A.O'Brochta (2009).
Hermes transposon distribution and structure in Musca domestica.
  J Hered, 100, 473-480.  
19174482 W.Bao, M.G.Jurka, V.V.Kapitonov, and J.Jurka (2009).
New superfamilies of eukaryotic DNA transposons and their internal divisions.
  Mol Biol Evol, 26, 983-993.  
19018586 A.Hua-Van, and P.Capy (2008).
Analysis of the DDE motif in the Mutator superfamily.
  J Mol Evol, 67, 670-681.  
18234093 P.De, S.Zhao, L.M.Gwyn, L.J.Godderz, M.M.Peak, and K.K.Rodgers (2008).
Thermal dependency of RAG1 self-association properties.
  BMC Biochem, 9, 5.  
18354502 R.Mitra, J.Fain-Thornton, and N.L.Craig (2008).
piggyBac can bypass DNA synthesis during cut and paste transposition.
  EMBO J, 27, 1097-1109.  
16912840 B.Brillet, B.Benjamin, Y.Bigot, B.Yves, C.Augé-Gouillou, and A.G.Corinne (2007).
Assembly of the Tc1 and mariner transposition initiation complexes depends on the origins of their transposase DNA binding domains.
  Genetica, 130, 105-120.  
17209048 D.Yamashita, H.Komori, Y.Higuchi, T.Yamaguchi, T.Osumi, and F.Hirose (2007).
Human DNA replication-related element binding factor (hDREF) self-association via hATC domain is necessary for its nuclear accumulation and DNA binding.
  J Biol Chem, 282, 7563-7575.  
17307873 G.J.Grundy, J.E.Hesse, and M.Gellert (2007).
Requirements for DNA hairpin formation by RAG1/2.
  Proc Natl Acad Sci U S A, 104, 3078-3083.  
17412704 J.Bischerour, and R.Chalmers (2007).
Base-flipping dynamics in a DNA hairpin processing reaction.
  Nucleic Acids Res, 35, 2584-2595.  
17644523 M.Tang, C.Cecconi, C.Bustamante, and D.C.Rio (2007).
Analysis of P element transposase protein-DNA interactions during the early stages of transposition.
  J Biol Chem, 282, 29002-29012.  
17984973 T.Wicker, F.Sabot, A.Hua-Van, J.L.Bennetzen, P.Capy, B.Chalhoub, A.Flavell, P.Leroy, M.Morgante, O.Panaud, E.Paux, P.SanMiguel, and A.H.Schulman (2007).
A unified classification system for eukaryotic transposable elements.
  Nat Rev Genet, 8, 973-982.  
17003053 C.Loot, N.Santiago, A.Sanz, and J.M.Casacuberta (2006).
The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs.
  Nucleic Acids Res, 34, 5238-5246.  
17028591 C.P.Lu, H.Sandoval, V.L.Brandt, P.A.Rice, and D.B.Roth (2006).
Amino acid residues in Rag1 crucial for DNA hairpin formation.
  Nat Struct Mol Biol, 13, 1010-1015.  
17096595 D.Balciunas, K.J.Wangensteen, A.Wilber, J.Bell, A.Geurts, S.Sivasubbu, X.Wang, P.B.Hackett, D.A.Largaespada, R.S.McIvor, and S.C.Ekker (2006).
Harnessing a high cargo-capacity transposon for genetic applications in vertebrates.
  PLoS Genet, 2, e169.  
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
16322520 M.A.Chesney, A.R.Kidd, and J.Kimble (2006).
gon-14 functions with class B and class C synthetic multivulva genes to control larval growth in Caenorhabditis elegans.
  Genetics, 172, 915-928.  
17130173 M.M.Babu, L.M.Iyer, S.Balaji, and L.Aravind (2006).
The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons.
  Nucleic Acids Res, 34, 6505-6520.  
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.

 

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