Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
6  structures 165  species 2  interactions 352  sequences 7  architectures

Family: Dimer_Tnp_Tn5 (PF02281)

Summary: Transposase Tn5 dimerisation domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Transposase". More...

Transposase Edit Wikipedia article

Transposase is an enzyme that binds to the end of a transposon and catalyzes its movement to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism. The word "transposase" was first coined by the individuals who cloned the enzyme required for transposition of the Tn3 transposon.[1] The existence of transposons was postulated in the late 1940s by Barbara McClintock, who was studying the inheritance of maize, but the actual molecular basis for transposition was described by later groups. McClintock discovered that pieces of the chromosomes changed their position, jumping from one chromosome to another. The repositioning of these transposons (which coded for color) allowed other genes for pigment to be expressed.[2] Transposition in maize causes changes in color; however, in other organisms, such as bacteria, it can cause antibiotic resistance.[2] Transposition is also important in creating genetic diversity within species and adaptability to changing living conditions.[3] During the course of human evolution, as much as 40% of the human genome has moved around via methods such as transposition of transposons.[2]

Transposases are classified under EC number EC 2.7.7.

Genes encoding transposases are widespread in the genomes of most organisms and are the most abundant genes known.[4]

Transposase Tn5

Transposase Tn5 dimerisation domain
PDB 1mur EBI.jpg
tn5 transposase: 20mer outside end 2 mn complex

Transposase (Tnp) Tn5 is a member of the RNase superfamily of proteins which includes retroviral integrases. Tn5 can be found in Shewanella and Escherichia bacteria.[5] The transposon codes for antibiotic resistance to kanamycin and other aminoglycoside antibiotics.[3][6]

Tn5 and other transposases are notably inactive. Because DNA transposition events are inherently mutagenic, the low activity of transposases is necessary to reduce the risk of causing a fatal mutation in the host, and thus eliminating the transposable element. One of the reasons Tn5 is so unreactive is because the N- and C-termini are located in relatively close proximity to one another and tend to inhibit each other. This was elucidated by the characterization of several mutations which resulted in hyperactive forms of transposases. One such mutation, L372P, is a mutation of amino acid 372 in the Tn5 transposase. This amino acid is generally a leucine residue in the middle of an alpha helix. When this leucine is replaced with a proline residue the alpha helix is broken, introducing a conformational change to the C-Terminal domain, separating it from the N-Terminal domain enough to promote higher activity of the protein.[3] The transposition of a transposon often needs only three pieces: the transposon, the transposase enzyme, and the target DNA for the insertion of the transposon.[3] This is the case with Tn5, which uses a cut-and-paste mechanism for moving around transposons.[3]

Tn5 and most other transposases contain a DDE motif, which is the active site that catalyzes the movement of the transposon. Aspartate-97, Aspartate-188, and Glutamate-326 make up the active site, which is a triad of acidic residues.[7] The DDE motif is said to coordinate divalent metal ions, most often magnesium and manganese, which are important in the catalytic reaction.[7] Because transposase is incredibly inactive, the DDE region is mutated so that the transposase becomes hyperactive and catalyzes the movement of the transposon.[7] The glutamate is transformed into an aspartate and the two aspartates into glutamates.[7] Through this mutation, the study of Tn5 becomes possible, but some steps in the catalytic process are lost as a result.[3]


There are several steps which catalyze the movement of the transposon, including Tnp binding, synapsis (the creation of a synaptic complex), cleavage, target capture, and strand transfer. Transposase then binds to the DNA strand and creates a clamp over the transposon end of the DNA and inserts into the active site. Once the transposase binds to the transposon, it produces a synaptic complex in which two transposases are bound in a cis/trans relationship with the transposon.[3]

In cleavage, the magnesium ions activate oxygen from water molecules and expose them to nucleophilic attack.[6] This allows the water molecules to nick the 3' strands on both ends and create a hairpin formation, which separates the transposon from the donor DNA.[3] Next, the transposase moves the transposon to a suitable location. Not much is known about the target capture, although there is a sequence bias which has not yet been determined.[3] After target capture, the transposase attacks the target DNA nine base pairs apart, resulting in the integration of the transposon into the target DNA.[3]

As mentioned before, due to the mutations of the DDE, some steps of the process are lost—for example, when this experiment is performed in vitro, and SDS heat treatment denatures the transposase. However, it is still uncertain what happens to the transposase in vivo.[3]

The study of transposase Tn5 is of general importance because of its similarities to HIV-1 and other retroviral diseases. By studying Tn5, much can also be discovered about other transposases and their activities.[3]

Tn5 is utilized in genome sequencing for fragmentation of the DNA, in the technique called ATAC-seq and also in Illumina dye sequencing.

Sleeping Beauty transposase

The Sleeping Beauty (SB) transposase is the recombinase that drives the Sleeping Beauty transposon system.[8] SB transposase belongs to the DD[E/D] family of transposases, which in turn belong to a large superfamily of polynucleotidyl transferases that includes RNase H, RuvC Holliday resolvase, RAG proteins, and retroviral integrases.[9][10] The SB system is used primarily in vertebrate animals for gene transfer,[11] including gene therapy,[12][13] and gene discovery.[14][15] The engineered SB100X is an enzyme that directs the high levels of transposon integration.[16][17]


  1. ^ Heffron F, McCarthy BJ, Ohtsubo H, Ohtsubo E (December 1979). "DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3". Cell. 18 (4): 1153–63. doi:10.1016/0092-8674(79)90228-9. PMID 391406.
  2. ^ a b c Goodsell D (December 2006). "Transposase". Molecule of the Month. Protein Data Bank.
  3. ^ a b c d e f g h i j k l Reznikoff WS (March 2003). "Tn5 as a model for understanding DNA transposition". Molecular Microbiology. 47 (5): 1199–206. doi:10.1046/j.1365-2958.2003.03382.x. PMID 12603728.
  4. ^ Aziz, R.K., M. Breitbart and R.A. Edwards (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic Acids Research 38(13): 4207-4217.Aziz RK, Breitbart M, Edwards RA (July 2010). "Transposases are the most abundant, most ubiquitous genes in nature". Nucleic Acids Research. 38 (13): 4207–17. doi:10.1093/nar/gkq140. PMC 2910039. PMID 20215432.
  5. ^ McDowall J. "Transposase". InterPro.
  6. ^ a b Lovell S, Goryshin IY, Reznikoff WR, Rayment I (April 2002). "Two-metal active site binding of a Tn5 transposase synaptic complex". Nature Structural Biology. 9 (4): 278–81. doi:10.1038/nsb778. PMID 11896402.
  7. ^ a b c d Peterson G, Reznikoff W (January 2003). "Tn5 transposase active site mutations suggest position of donor backbone DNA in synaptic complex". The Journal of Biological Chemistry. 278 (3): 1904–9. doi:10.1074/jbc.M208968200. PMID 12424243.
  8. ^ Ivics, Z.; Hackett, P.B.; Plasterk, R.A.; Izsvak, Z. (1997). "Molecular reconstruction of Sleeping Beauty: a Tc1-like transposon from fish and its transposition in human cells". Cell. 91 (4): 501–510. doi:10.1016/s0092-8674(00)80436-5. PMID 9390559.
  9. ^ Craig NL (October 1995). "Unity in transposition reactions". Science. 270 (5234): 253–4. doi:10.1126/science.270.5234.253. PMID 7569973.
  10. ^ Nesmelova IV, Hackett PB (September 2010). "DDE transposases: Structural similarity and diversity". Advanced Drug Delivery Reviews. 62 (12): 1187–95. doi:10.1016/j.addr.2010.06.006. PMC 2991504. PMID 20615441.
  11. ^ Ivics Z, Izsvák Z (January 2005). "A whole lotta jumpin' goin' on: new transposon tools for vertebrate functional genomics". Trends in Genetics. 21 (1): 8–11. doi:10.1016/j.tig.2004.11.008. PMID 15680506.
  12. ^ Izsvák Z, Hackett PB, Cooper LJ, Ivics Z (September 2010). "Translating Sleeping Beauty transposition into cellular therapies: victories and challenges". BioEssays. 32 (9): 756–67. doi:10.1002/bies.201000027. PMC 3971908. PMID 20652893.
  13. ^ Aronovich, E.L., McIvor, R.S., and Hackett, P.B. (2011). The Sleeping Beauty transposon system – A non-viral vector for gene therapy. Hum. Mol. Genet. (in press)Aronovich EL, McIvor RS, Hackett PB (April 2011). "The Sleeping Beauty transposon system: a non-viral vector for gene therapy". Human Molecular Genetics. 20 (R1): R14–20. doi:10.1093/hmg/ddr140. PMC 3095056. PMID 21459777.
  14. ^ Carlson CM, Largaespada DA (July 2005). "Insertional mutagenesis in mice: new perspectives and tools". Nature Reviews Genetics. 6 (7): 568–80. doi:10.1038/nrg1638. PMID 15995698.
  15. ^ Copeland NG, Jenkins NA (October 2010). "Harnessing transposons for cancer gene discovery". Nature Reviews. Cancer. 10 (10): 696–706. doi:10.1038/nrc2916. PMID 20844553.
  16. ^ Mátés L, Chuah MK, Belay E, Jerchow B, Manoj N, Acosta-Sanchez A, et al. (June 2009). "Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates". Nature Genetics. 41 (6): 753–61. doi:10.1038/ng.343. PMID 19412179.
  17. ^ Grabundzija I, Irgang M, Mátés L, Belay E, Matrai J, Gogol-Döring A, Kawakami K, Chen W, Ruiz P, Chuah MK, VandenDriessche T, Izsvák Z, Ivics Z (June 2010). "Comparative analysis of transposable element vector systems in human cells". Molecular Therapy. 18 (6): 1200–9. doi:10.1038/mt.2010.47. PMC 2889740. PMID 20372108.

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Transposase Tn5 dimerisation domain Provide feedback

Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyses insertion, found between terminal inverted repeats. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor [1]. The catalytic domain of the Tn5 transposon is found in PF01609. This domain mediates dimerisation in the known structure.

Literature references

  1. Davies DR, Braam LM, Reznikoff WS, Rayment I; , J Biol Chem 1999;274:11904-11913.: The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. PUBMED:10207011 EPMC:10207011

  2. Johnson RC, Reznikoff WS; , Nature 1983;304:280-282.: DNA sequences at the ends of transposon Tn5 required for transposition. PUBMED:6306482 EPMC:6306482

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003201

Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyses insertion, found between terminal inverted repeats [PUBMED:6306482]. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor [PUBMED:10207011].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_5683 (release 5.2)
Previous IDs: Transposase_Tn5;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 2
Number in full: 352
Average length of the domain: 89.10 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 25.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 26.7 26.7
Noise cut-off 26.5 26.5
Model length: 103
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


There are 2 interactions for this family. More...

Tnp_DNA_bind DDE_Tnp_1


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Dimer_Tnp_Tn5 domain has been found. There are 6 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...