Summary: DNA gyrase/topoisomerase IV, subunit A
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DNA gyrase/topoisomerase IV, subunit A Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | NTase_sub_bind |
External database links
HOMSTRAD: | DNA_topoisoIV |
SCOP: | 1bgw |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002205
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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils [PUBMED:7980433].
Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [PUBMED:8982450].
Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [PUBMED:16023670]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.
This entry represents subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent C-terminal region in eukaryotic topoisomerase II composed of a single polypeptide. This subunit has DNA-binding capacity.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | DNA binding (GO:0003677) |
ATP binding (GO:0005524) | |
DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity (GO:0003918) | |
Biological process | DNA topological change (GO:0006265) |
Domain organisation
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Alignments
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Seed (78) |
Full (14995) |
Representative proteomes | UniProt (73024) |
NCBI (97059) |
Meta (6518) |
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RP15 (2231) |
RP35 (7375) |
RP55 (14709) |
RP75 (24731) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (78) |
Full (14995) |
Representative proteomes | UniProt (73024) |
NCBI (97059) |
Meta (6518) |
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RP15 (2231) |
RP35 (7375) |
RP55 (14709) |
RP75 (24731) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Trees
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Curation and family details
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Curation
Seed source: | Pfam-B_55 (release 1.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Finn RD |
Number in seed: | 78 |
Number in full: | 14995 |
Average length of the domain: | 433.60 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 48.83 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 426 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 6 interactions for this family. More...
DNA_topoisoIV DNA_gyraseB_C Toprim CcdB DNA_gyraseB_C ToprimStructures
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 DNA_topoisoIV domain has been found. There are 251 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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