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0  structures 3740  species 0  interactions 10157  sequences 102  architectures

Family: zf-C4_Topoisom (PF01396)

Summary: Topoisomerase DNA binding C4 zinc finger

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Topoisomerase DNA binding C4 zinc finger Provide feedback

No Pfam abstract.

Literature references

  1. Tse-Dinh YC, Beran-Steed RK; , J Biol Chem 1988;263:15857-15859.: Escherichia coli DNA topoisomerase I is a zinc metalloprotein with three repetitive zinc-binding domains. PUBMED:2846526 EPMC:2846526

  2. Ahumada A, Tse-Dinh YC; , Biochem Biophys Res Commun 1998;251:509-514.: The Zn(II) binding motifs of E. coli DNA topoisomerase I is part of a high-affinity DNA binding domain. PUBMED:9792804 EPMC:9792804


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013498

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 (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type 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 entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc [PUBMED:10873443]. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc.

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

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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
(27)
Full
(10157)
Representative proteomes NCBI
(7084)
Meta
(1633)
RP15
(613)
RP35
(1165)
RP55
(1614)
RP75
(1974)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(27)
Full
(10157)
Representative proteomes NCBI
(7084)
Meta
(1633)
RP15
(613)
RP35
(1165)
RP55
(1614)
RP75
(1974)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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.

  Seed
(27)
Full
(10157)
Representative proteomes NCBI
(7084)
Meta
(1633)
RP15
(613)
RP35
(1165)
RP55
(1614)
RP75
(1974)
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: Pfam-B_1854 (release 3.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 27
Number in full: 10157
Average length of the domain: 39.50 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 11.65 %

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 20.5
Noise cut-off 20.4 20.4
Model length: 39
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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