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7  structures 417  species 1  interaction 534  sequences 9  architectures

Family: TP6A_N (PF04406)

Summary: Type IIB DNA topoisomerase

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Type IIB DNA topoisomerase Provide feedback

Type II DNA topoisomerases are ubiquitous enzymes that catalyse the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP) [1].

Literature references

  1. Nichols MD, DeAngelis K, Keck JL, Berger JM; , EMBO J 1999;18:6177-6188.: Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. PUBMED:10545127 EPMC:10545127


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013049

This entry represents the N-terminal domain found in Spo11, a meiotic recombination protein found in eukaryotes, and in subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [PUBMED:10545127, PUBMED:12618182]. These two types of proteins share structural homology.

Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination [PUBMED:11805049].

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (EC, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (EC, topoisomerases II, IV and VI) break double-strand DNA [PUBMED:12596227]. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein.

More information about this protein can be found at Protein of the Month: DNA Topoisomerase [PUBMED:].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(65)
Full
(534)
Representative proteomes NCBI
(531)
Meta
(120)
RP15
(105)
RP35
(197)
RP55
(287)
RP75
(349)
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Format an alignment

  Seed
(65)
Full
(534)
Representative proteomes NCBI
(531)
Meta
(120)
RP15
(105)
RP35
(197)
RP55
(287)
RP75
(349)
Alignment:
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Sequence:
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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.

  Seed
(65)
Full
(534)
Representative proteomes NCBI
(531)
Meta
(120)
RP15
(105)
RP35
(197)
RP55
(287)
RP75
(349)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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...

Trees

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: COG1697
Previous IDs: none
Type: Domain
Author: Waterfield DI, Finn RD
Number in seed: 65
Number in full: 534
Average length of the domain: 69.40 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 18.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.5 20.8
Noise cut-off 20.2 20.4
Model length: 68
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Topo-VIb_trans

Structures

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 TP6A_N domain has been found. There are 7 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 seqence.

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