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61  structures 4388  species 1  interaction 33006  sequences 51  architectures

Family: DNA_gyraseA_C (PF03989)

Summary: DNA gyrase C-terminal domain, beta-propeller

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DNA gyrase C-terminal domain, beta-propeller Provide feedback

This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure [1]. This region has been shown to bind DNA non-specifically and may stabilise the DNA-topoisomerase complex [2].

Literature references

  1. Qi Y, Pei J, Grishin NV; , Proteins 2002;47:258-264.: C-terminal domain of gyrase A is predicted to have a beta-propeller structure. PUBMED:11948780 EPMC:11948780

  2. Reece RJ, Maxwell A; , Crit Rev Biochem Mol Biol 1991;26:335-375.: DNA gyrase: structure and function. PUBMED:1657531 EPMC:1657531


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006691

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].

This entry represents the beta-pinwheel repeat found at the C-terminal end of subunit A of topoisomerase IV (ParC) and subunit A of DNA gyrase (GyrA). DNA gyrase is the topoisomerase II found primarily in bacteria and archaea that consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. This is distinct from the topoisomerase II found in most eukaryotes, which consists of a single polypeptide, with the N- and C-terminal regions corresponding to gyrB and gyrA, respectively, and which is not represented in this entry.

The ability of DNA gyrase to introduce negative supercoils into DNA is mediated in part by the C-terminal domain of subunit A, which forms a beta-pinwheel fold that is similar to a beta-propeller but with a different blade topology, and which forms a superhelical spiral domain [PUBMED:15123801, PUBMED:15897198]. This beta-pinwheel is capable of bending DNA by over 180 degrees over a 40 bp region, possibly by wrapping the DNA around the GyrA C-terminal beta-pinwheel domain.

In topoisomerase IV, although the C-terminal domain forms a similar superhelical spiral to that of DNA gyrase A, it assembles as a broken form of a beta-pinwheel as distinct from that of gyrA, due to the absence of a DNA gyrase-specific GyrA box motif [PUBMED:15466871]. This difference may account for parC being less efficient than gyrA in mediating DNA-bending, leading to their divergence in terms of activity, where topoisomerase IV acts to relax positive supercoils, and DNA gyrase acts to introduce negative supercoils [PUBMED:16023670].

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
(217)
Full
(33006)
Representative proteomes UniProt
(102007)
NCBI
(173939)
Meta
(14599)
RP15
(6782)
RP35
(19724)
RP55
(33608)
RP75
(51874)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(217)
Full
(33006)
Representative proteomes UniProt
(102007)
NCBI
(173939)
Meta
(14599)
RP15
(6782)
RP35
(19724)
RP55
(33608)
RP75
(51874)
Alignment:
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  Seed
(217)
Full
(33006)
Representative proteomes UniProt
(102007)
NCBI
(173939)
Meta
(14599)
RP15
(6782)
RP35
(19724)
RP55
(33608)
RP75
(51874)
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.

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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: Yeats C
Previous IDs: none
Type: Repeat
Author: Yeats C
Number in seed: 217
Number in full: 33006
Average length of the domain: 47.20 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 27.58 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 5.9
Trusted cut-off 27.0 5.9
Noise cut-off 26.9 5.8
Model length: 48
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

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

DNA_gyraseA_C

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 DNA_gyraseA_C domain has been found. There are 61 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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