Summary: DNA gyrase B
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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
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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
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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
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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
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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
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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
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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
PRINTS: | PR00418 |
PROSITE: | PDOC00160 |
SCOP: | 1bgw |
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.
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
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_NAlignments
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.
Seed (48) |
Full (18233) |
Representative proteomes | UniProt (99580) |
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RP15 (2855) |
RP35 (9022) |
RP55 (18197) |
RP75 (30198) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (48) |
Full (18233) |
Representative proteomes | UniProt (99580) |
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RP15 (2855) |
RP35 (9022) |
RP55 (18197) |
RP75 (30198) |
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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.
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
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Curation
Seed source: | SCOP |
Previous IDs: | DNA_topoisoII; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 174 | ||||||||||||
Family (HMM) version: | 28 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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_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.