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17  structures 1087  species 2  interactions 1548  sequences 25  architectures

Family: Topoisom_I_N (PF02919)

Summary: Eukaryotic DNA topoisomerase I, DNA binding fragment

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Eukaryotic DNA topoisomerase I, DNA binding fragment Provide feedback

Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination [2]. This family may be more than one structural domain.

Literature references

  1. Roca J; , Trends Biochem Sci 1995;20:156-160.: The mechanisms of DNA topoisomerases. PUBMED:7770916 EPMC:7770916

  2. Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG; , Science 1998;279:1504-1513.: Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. PUBMED:9488644 EPMC:9488644


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008336

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 [PUBMED:7770916]. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [PUBMED:12042765, PUBMED:11395412]. DNA topoisomerases are 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].

Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo IB; eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [PUBMED:17293019]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [PUBMED:21087076,PUBMED:9488644]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [PUBMED:20644584,PUBMED:17722649].

This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain [PUBMED:14741206]. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes [PUBMED:9488644].

Gene Ontology

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Domain organisation

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Alignments

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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
(137)
Full
(1548)
Representative proteomes UniProt
(3900)
NCBI
(4185)
Meta
(28)
RP15
(439)
RP35
(846)
RP55
(1196)
RP75
(1433)
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  Seed
(137)
Full
(1548)
Representative proteomes UniProt
(3900)
NCBI
(4185)
Meta
(28)
RP15
(439)
RP35
(846)
RP55
(1196)
RP75
(1433)
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
(137)
Full
(1548)
Representative proteomes UniProt
(3900)
NCBI
(4185)
Meta
(28)
RP15
(439)
RP35
(846)
RP55
(1196)
RP75
(1433)
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

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_1377 (release 3.0)
Previous IDs: Topoisomer_I_N;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 137
Number in full: 1548
Average length of the domain: 205.70 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 27.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.8 25.5
Noise cut-off 24.8 22.4
Model length: 213
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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

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Interactions

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

Topoisom_I Topo_C_assoc

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 Topoisom_I_N domain has been found. There are 17 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.

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