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Entry version 100 (08 May 2019)
Sequence version 3 (23 Jan 2007)
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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Staphylococcus aureus (strain COL)
Status
Reviewed-Annotation score:

Annotation score:3 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>
-Protein inferred from homologyi <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 that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

Miscellaneous

Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 annotation EC:5.6.2.3

<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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 bindingi435Magnesium 1; catalyticUniRule annotation1
Metal bindingi508Magnesium 1; catalyticUniRule annotation1
Metal bindingi508Magnesium 2UniRule annotation1
Metal bindingi510Magnesium 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
SAUR93062:G1G4B-5-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_and_taxonomy_section">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:
DNA gyrase subunit BUniRule annotation (EC:5.6.2.3UniRule annotation)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:SACOL0005
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiStaphylococcus aureus (strain COL)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri93062 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000000530 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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

GO - Cellular componenti

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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedBy similarity
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001453372 – 644DNA gyrase subunit BAdd BLAST643

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q5HJZ1

<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_section">'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_section">'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.

UniRule annotation

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>Sitei460Interaction with DNAUniRule annotation1
Sitei463Interaction with DNAUniRule annotation1

<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
Q5HJZ1

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_and_domains_section">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>Domaini429 – 543ToprimUniRule 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
ENOG4105C7D Bacteria
COG0187 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000075154

KEGG Orthology (KO)

More...
KOi
K02470

Identification of Orthologs from Complete Genome Data

More...
OMAi
IYIACPP

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00075 HATPase_c, 1 hit
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, 1 hit

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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q5HJZ1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVTALSDVNN TDNYGAGQIQ VLEGLEAARK RPGMYIGSTS ERGLHHLVWE
60 70 80 90 100
IVDNSIDEAL AGYANQIEVV IEKDNWIKVT DNGRGIPVDI QEKMGRPAVE
110 120 130 140 150
VILTVLHAGG KFGGGGYKVS GGLHGVGSSV VNALSQDLEV YVHRNETIYH
160 170 180 190 200
QAYKKGVPQF DLKEVGTTDK TGTVIRFKAD GEIFTETTVY NYETLQQRIR
210 220 230 240 250
ELAFLNKGIQ ITLRDERDEE NVREDSYHYE GGIKSYVELL NENKEPIHDE
260 270 280 290 300
PIYIHQSKDD IEVEIAIQYN SGYATNLLTY ANNIHTYEGG THEDGFKRAL
310 320 330 340 350
TRVLNSYGLS SKIMKEEKDR LSGEDTREGM TAIISIKHGD PQFEGQTKTK
360 370 380 390 400
LGNSEVRQVV DKLFSEHFER FLYENPQVAR TVVEKGIMAA RARVAAKKAR
410 420 430 440 450
EVTRRKSALD VASLPGKLAD CSSKSPEECE IFLVEGDSAG GSTKSGRDSR
460 470 480 490 500
TQAILPLRGK ILNVEKARLD RILNNNEIRQ MITAFGTGIG GDFDLAKARY
510 520 530 540 550
HKIVIMTDAD VDGAHIRTLL LTFFYRFMRP LIEAGYVYIA QPPLYKLTQG
560 570 580 590 600
KQKYYVYNDR ELDKLKSELN PTPKWSIARY KGLGEMNADQ LWETTMNPEH
610 620 630 640
RALLQVKLED AIEADQTFEM LMGDVVENRR QFIEDNAVYA NLDF
Length:644
Mass (Da):72,512
Last modified:January 23, 2007 - v3
<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:iB4E0D0D87899D90A
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
CP000046 Genomic DNA Translation: AAW37393.1

NCBI Reference Sequences

More...
RefSeqi
WP_000255576.1, NC_002951.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAW37393; AAW37393; SACOL0005

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sac:SACOL0005

<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
CP000046 Genomic DNA Translation: AAW37393.1
RefSeqiWP_000255576.1, NC_002951.2

3D structure databases

SMRiQ5HJZ1
ModBaseiSearch...

Proteomic databases

PRIDEiQ5HJZ1

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAW37393; AAW37393; SACOL0005
KEGGisac:SACOL0005

Phylogenomic databases

eggNOGiENOG4105C7D Bacteria
COG0187 LUCA
HOGENOMiHOG000075154
KOiK02470
OMAiIYIACPP

Enzyme and pathway databases

BioCyciSAUR93062:G1G4B-5-MONOMER

Family and domain databases

CDDicd00075 HATPase_c, 1 hit
cd03366 TOPRIM_TopoIIA_GyrB, 1 hit
Gene3Di3.30.230.10, 1 hit
3.30.565.10, 1 hit
3.40.50.670, 1 hit
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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiGYRB_STAAC
<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: Q5HJZ1
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: January 23, 2007
Last modified: May 8, 2019
This is version 100 of the entry and version 3 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

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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