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44  structures 3525  species 0  interactions 12818  sequences 91  architectures

Clan: HUH (CL0481)


His-hydrophobic-His tranposase Y1,Y2 superfamily Add an annotation

This superfamily consists of families of transposases that use tyrosine as nucleophiles and contain a conserved HUH motif where U is a non-conserved hydrophobic residue. Particular examples are the Y1 and Y2 transposases. Y1 transposases come from the IS608 group and the Y2 from the IS91 group. These transposases are nucleases involved in initiating rolling-circle plasmid replication, in initiating replication of certain single-strand (ss) DNA viruses (Rep proteins), and in initiation of conjugative plasmid transfer (relaxases). The IS91 transposase contains two of the three conserved protein sequence motifs identified in RCR proteins, a His-hydrophobic-His (HUH) motif required for metal ion binding, and a YxxxY motif containing two conserved catalytic tyrosine residues. The HUH motif participates in coordinating divalent metal ions essential for catalysis. This clan is also known as the Transposase IS200-like whose members contain extra N-terminal hairpin and C-terminal helix, both or which are involved in dimerisation; there can be helix-swapping in the dimer.

This clan contains 2 families and the total number of domains in the clan is 12818. The clan was built by P Coggill.

Literature references

  1. Lee HH, Yoon JY, Kim HS, Kang JY, Kim KH, Kim DJ, Ha JY, Mikami B, Yoon HJ, Suh SW; , J Biol Chem. 2006;281:4261-4266.: Crystal structure of a metal ion-bound IS200 transposase. PUBMED:16340015 EPMC:16340015


This clan contains the following 2 member families:

Y1_Tnp Y2_Tnp

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
Y1_Tnp (PF01797) 10737 (83.8%) View
Y2_Tnp (PF04986) 2081 (16.2%) View
Total: 2 Total: 12818 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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