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123  structures 8981  species 0  interactions 18233  sequences 140  architectures

Family: DNA_gyraseB (PF00204)

Summary: DNA gyrase B

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DNA gyrase B Provide feedback

This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.

Literature references

  1. Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G; , Nature 1991;351:624-629.: Crystal structure of an N-terminal fragment of the DNA gyrase B protein. PUBMED:1646964 EPMC:1646964

  2. Brino L, Urzhumtsev A, Mousli M, Bronner C, Mitschler A, Oudet P, Moras D , J Biol Chem 2000;275:9468-9475.: Dimerization of Escherichia coli DNA-gyrase B provides a structural mechanism for activating the ATPase catalytic center. PUBMED:10734094 EPMC:10734094

  3. Brino L, Bronner C, Oudet P, Mousli M , Biochimie 1999;81:973-980.: Isoleucine 10 is essential for DNA gyrase B function in Escherichia coli. PUBMED:10575351 EPMC:10575351

  4. Tanaka T, Saha SK, Tomomori C, Ishima R, Liu D, Tong KI, Park H, Dutta R, Qin L, Swindells MB, Yamazaki T, Ono AM, Kainosho M, Inouye M, Ikura M , Nature 1998;396:88-92.: NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ. PUBMED:9817206 EPMC:9817206

  5. Smith CV, Maxwell A , Biochemistry 1998;37:9658-9667.: Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase. PUBMED:9657678 EPMC:9657678

  6. Prodromou C, Roe SM, O'Brien R, Ladbury JE, Piper PW, Pearl LH , Cell 1997;90:65-75.: Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. PUBMED:9230303 EPMC:9230303

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013506

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, 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 the second domain found in subunit B (gyrB and parE) of bacterial gyrase and topoisomerase IV, and the equivalent N-terminal region in eukaryotic topoisomerase II composed of a single polypeptide.

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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Pfam Clan

This family is a member of clan S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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

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: SCOP
Previous IDs: DNA_topoisoII;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 48
Number in full: 18233
Average length of the domain: 171.6 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 21.29 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.7
Model length: 174
Family (HMM) version: 28
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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_gyraseB domain has been found. There are 123 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044S7T8 View 3D Structure Click here
A0A044V129 View 3D Structure Click here
A0A044VHS1 View 3D Structure Click here
A0A077Z5V9 View 3D Structure Click here
A0A077Z7T8 View 3D Structure Click here
A0A077ZBW5 View 3D Structure Click here
A0A077ZE75 View 3D Structure Click here
A0A077ZFT4 View 3D Structure Click here
A0A077ZIN2 View 3D Structure Click here
A0A0D2H7P4 View 3D Structure Click here
A0A0H3GXR6 View 3D Structure Click here
A0A0H3H365 View 3D Structure Click here
A0A0J9XU95 View 3D Structure Click here
A0A0K0DSA3 View 3D Structure Click here
A0A0K0DVI2 View 3D Structure Click here
A0A0K0EEJ7 View 3D Structure Click here
A0A0K0JTZ4 View 3D Structure Click here
A0A0N4U200 View 3D Structure Click here
A0A0N4UJB6 View 3D Structure Click here
A0A0R4IUF0 View 3D Structure Click here
A0A175VTD9 View 3D Structure Click here
A0A1C1CFC8 View 3D Structure Click here
A0A1D6HGU3 View 3D Structure Click here
A0A1D6Q7T3 View 3D Structure Click here
A0A1D8PMM1 View 3D Structure Click here
A0A1P6C3R4 View 3D Structure Click here
A0A1P8BB88 View 3D Structure Click here
A0A3P7DD04 View 3D Structure Click here
A0A3P7DE40 View 3D Structure Click here
A0A3P7FC77 View 3D Structure Click here
A0A3Q0KH18 View 3D Structure Click here
A0QNE0 View 3D Structure Click here
A0QPN2 View 3D Structure Click here
A4HWL4 View 3D Structure Click here
A4I3V9 View 3D Structure Click here
B8GXQ0 View 3D Structure Click here
C0NX13 View 3D Structure Click here
C0P6Q6 View 3D Structure Click here
C1GXB2 View 3D Structure Click here
C5C7X8 View 3D Structure Click here