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Entry version 135 (02 Dec 2020)
Sequence version 1 (01 Aug 1998)
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Protein

Type 2 topoisomerase subunit B

Gene

gyrB

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

A type II topoisomerase. Despite its similarity to DNA gyrase, this enzyme is not able to supercoil DNA, and instead acts like topoisomerase IV. Relaxes both positively and negatively supercoiled DNA in an ATP-dependent fashion, decatenates interlocked circles. If this subunit is reconstituted with GyrA from E.coli the hybrid enzyme supercoils relaxed plasmid DNA; if paired with E.coli ParC supercoiling is not restored. This the first bacteria shown to not contain DNA gyrase, although it has 2 copies of a reverse gyrase that introduces positive supercoils. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner (PubMed:21076033).

1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation1 Publication EC:5.6.2.2

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ or Ca2+.UniRule annotation

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Temperature dependencei

Optimum temperature is 70 degrees Celsius, active between 37 and 90 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi429Magnesium 1; catalyticUniRule annotation1
Metal bindingi502Magnesium 1; catalyticUniRule annotation1
Metal bindingi502Magnesium 2UniRule annotation1
Metal bindingi504Magnesium 2UniRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
AAEO224324:G1G15-727-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Type 2 topoisomerase subunit B1 Publication (EC:5.6.2.2UniRule annotation1 Publication)
Alternative name(s):
DNA gyrase subunit B
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:aq_1026
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiAquifex aeolicus (strain VF5)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri224324 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000798 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001452891 – 792Type 2 topoisomerase subunit BAdd BLAST792

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, 'GyrA' contains the active site tyrosine that forms a transient covalent intermediate with DNA, while 'GyrB' binds cofactors and catalyzes ATP hydrolysis (PubMed:21076033).

UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei454Interaction with DNAUniRule annotation1
Sitei457Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224324.aq_1026

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
O67137

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini423 – 537ToprimUniRule annotationAdd BLAST115

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0187, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_006146_0_1_0

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O67137

Identification of Orthologs from Complete Genome Data

More...
OMAi
LWETTMH

Database of Orthologous Groups

More...
OrthoDBi
205481at2

Family and domain databases

Conserved Domains Database

More...
CDDi
cd03366, TOPRIM_TopoIIA_GyrB, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.230.10, 1 hit
3.30.565.10, 1 hit
3.40.50.670, 2 hits

HAMAP database of protein families

More...
HAMAPi
MF_01898, GyrB, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002288, DNA_gyrase_B_C
IPR011557, GyrB
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR020568, Ribosomal_S5_D2-typ_fold
IPR014721, Ribosomal_S5_D2-typ_fold_subgr
IPR001241, Topo_IIA
IPR013760, Topo_IIA-like_dom_sf
IPR013759, Topo_IIA_B_C
IPR013506, Topo_IIA_bsu_dom2
IPR018522, TopoIIA_CS
IPR006171, TOPRIM_domain
IPR034160, TOPRIM_GyrB

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00204, DNA_gyraseB, 1 hit
PF00986, DNA_gyraseB_C, 1 hit
PF02518, HATPase_c, 1 hit
PF01751, Toprim, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00387, HATPase_c, 1 hit
SM00433, TOP2c, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54211, SSF54211, 1 hit
SSF55874, SSF55874, 1 hit
SSF56719, SSF56719, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR01059, gyrB, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00177, TOPOISOMERASE_II, 1 hit
PS50880, TOPRIM, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

O67137-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKKRQSQTPQ EYTAEAIKAV SGLEHVRLRP AMYIGDIGER GLHHLIWEIL
60 70 80 90 100
DNAVDEAVAG YARNISVTIH RDNSVTVEDD GRGIPVDIHP ETGKPAVEMV
110 120 130 140 150
FTMLGAGGKF EKKVYTYSGG LHGVGASVVN ALSEWLIVEV YRDGKIYRMA
160 170 180 190 200
FKRGEVVEPL HVVGETKKRG TKVSFKPDPE IFETTEIKFD IVEKRVRELA
210 220 230 240 250
YLNPEVKFEL TDERLGKHLI YKFDRGIEEL VKYLNEGKEP LFKDIIRIQG
260 270 280 290 300
EKEGVIVDIA FQYVKDYKER IESFVNNIKT VEGGTHVTGF RSGLSKAVIR
310 320 330 340 350
MAQGLKLAKE LKKSFTGEDV REGLTAVVAC KVPNPQFEGQ TKTKLGNQNV
360 370 380 390 400
KQIVESITYD FLTSYFEKKR DVLKAIVEKA IEAALAREAA KKAKELVRRK
410 420 430 440 450
SPLEEGVLPG KLADCSETDP SKCEIFLVEG DSAGGSAKQA RDRRYQAILP
460 470 480 490 500
LRGKIINVEK ARIDKVLSND EIKAIVSALG CGIGEDLDLK KLRYHKIILM
510 520 530 540 550
TDADVDGSHI RTLLLTFFYR FMPKLVEEGY VYIAEPPLYR VKKGKKEIYI
560 570 580 590 600
KDDKEFEHFL LNEIREKGRL VDAREKEFKG EELVRLLIDL KDYEDAYRAL
610 620 630 640 650
VKSKGENLVN FLLTHRVREE DLRNPARVKE ITHLMEEELG DYRVDTKYNE
660 670 680 690 700
LEGAYDIIFY DDKLGTKTII DVNFLSSLSY REVLEGIHLH LPVQVFFENK
710 720 730 740 750
KVEINSLGEI YDKFMDFARS GMEVQRYKGL GEMNPEQLWE TTMNPKTRRL
760 770 780 790
KKVKIEDAAE ADRIFTILMG EQVEPRREFI EAYAKEVKHL DV
Length:792
Mass (Da):90,530
Last modified:August 1, 1998 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i07DC02DF293FF9F3
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AE000657 Genomic DNA Translation: AAC07098.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F70388

NCBI Reference Sequences

More...
RefSeqi
NP_213700.1, NC_000918.1
WP_010880638.1, NC_000918.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC07098; AAC07098; aq_1026

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
aae:aq_1026

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224324.8.peg.802

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA Translation: AAC07098.1
PIRiF70388
RefSeqiNP_213700.1, NC_000918.1
WP_010880638.1, NC_000918.1

3D structure databases

SMRiO67137
ModBaseiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1026

Genome annotation databases

EnsemblBacteriaiAAC07098; AAC07098; aq_1026
KEGGiaae:aq_1026
PATRICifig|224324.8.peg.802

Phylogenomic databases

eggNOGiCOG0187, Bacteria
HOGENOMiCLU_006146_0_1_0
InParanoidiO67137
OMAiLWETTMH
OrthoDBi205481at2

Enzyme and pathway databases

BioCyciAAEO224324:G1G15-727-MONOMER

Family and domain databases

CDDicd03366, TOPRIM_TopoIIA_GyrB, 1 hit
Gene3Di3.30.230.10, 1 hit
3.30.565.10, 1 hit
3.40.50.670, 2 hits
HAMAPiMF_01898, GyrB, 1 hit
InterProiView protein in InterPro
IPR002288, DNA_gyrase_B_C
IPR011557, GyrB
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR020568, Ribosomal_S5_D2-typ_fold
IPR014721, Ribosomal_S5_D2-typ_fold_subgr
IPR001241, Topo_IIA
IPR013760, Topo_IIA-like_dom_sf
IPR013759, Topo_IIA_B_C
IPR013506, Topo_IIA_bsu_dom2
IPR018522, TopoIIA_CS
IPR006171, TOPRIM_domain
IPR034160, TOPRIM_GyrB
PfamiView protein in Pfam
PF00204, DNA_gyraseB, 1 hit
PF00986, DNA_gyraseB_C, 1 hit
PF02518, HATPase_c, 1 hit
PF01751, Toprim, 1 hit
SMARTiView protein in SMART
SM00387, HATPase_c, 1 hit
SM00433, TOP2c, 1 hit
SUPFAMiSSF54211, SSF54211, 1 hit
SSF55874, SSF55874, 1 hit
SSF56719, SSF56719, 1 hit
TIGRFAMsiTIGR01059, gyrB, 1 hit
PROSITEiView protein in PROSITE
PS00177, TOPOISOMERASE_II, 1 hit
PS50880, TOPRIM, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTOP4B_AQUAE
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O67137
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: December 2, 2020
This is version 135 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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