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UniProtKB - P05653 (GYRA_BACSU)

Protein

DNA gyrase subunit A

Gene

gyrA

Organism
Bacillus subtilis (strain 168)
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>-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 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:5.99.1.3

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei123O-(5'-phospho-DNA)-tyrosine intermediateUniRule 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

  • ATP binding Source: GO_Central
  • DNA binding Source: GO_Central
  • DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-UniRule
View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

<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, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU00070-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 AUniRule annotation (EC:5.99.1.3UniRule 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:gyrAUniRule annotation
Synonyms:cafB, nalA
Ordered Locus Names:BSU00070
<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>OrganismiBacillus subtilis (strain 168)
<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 identifieri224308 [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 lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<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
  • UP000001570 <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

View the complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Chemistry databases

Drug and drug target database

More...DrugBanki		DB00537 Ciprofloxacin

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001452211 – 821DNA gyrase subunit AAdd BLAST821

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P05653

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P05653

PRoteomics IDEntifications database

More...PRIDEi		P05653

<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

Protein-protein interaction databases

Protein interaction database and analysis system

More...IntActi		P05653, 5 interactors

Molecular INTeraction database

More...MINTi		P05653

STRING: functional protein association networks

More...STRINGi		224308.Bsubs1_010100000035

Chemistry databases

BindingDB database of measured binding affinities

More...BindingDBi		P05653

<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

Secondary structure

1821
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4DDQX-ray3.30A/B/C/D/E/F1-502[»]

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...ProteinModelPortali		P05653

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

More...SMRi		P05653

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi527 – 533GyrA-boxUniRule annotation7

<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 GyrA/ParC subunit family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105C24 Bacteria
COG0188 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000076278

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P05653

KEGG Orthology (KO)

More...KOi		K02469

Identification of Orthologs from Complete Genome Data

More...OMAi		THHWLLF

Database for complete collections of gene phylogenies

More...PhylomeDBi		P05653

Family and domain databases

Conserved Domains Database

More...CDDi		cd00187 TOP4c, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.268.10, 1 hit
2.120.10.90, 1 hit
3.90.199.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01897 GyrA, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR005743 GyrA
IPR006691 GyrA/parC_rep
IPR035516 Gyrase/topoIV_suA_C
IPR013760 Topo_IIA-like_dom_sf
IPR002205 Topo_IIA_A/C
IPR013758 Topo_IIA_A/C_ab
IPR013757 Topo_IIA_A_a_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF03989 DNA_gyraseA_C, 6 hits
PF00521 DNA_topoisoIV, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00434 TOP4c, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF101904 SSF101904, 1 hit
SSF56719 SSF56719, 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>.<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.

P05653-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSEQNTPQVR EINISQEMRT SFLDYAMSVI VSRALPDVRD GLKPVHRRIL 
        60         70         80         90        100
YAMNDLGMTS DKPYKKSARI VGEVIGKYHP HGDSAVYESM VRMAQDFNYR 
       110        120        130        140        150
YMLVDGHGNF GSVDGDSAAA MRYTEARMSK ISMEILRDIT KDTIDYQDNY 
       160        170        180        190        200
DGSEREPVVM PSRFPNLLVN GAAGIAVGMA TNIPPHQLGE IIDGVLAVSE 
       210        220        230        240        250
NPDITIPELM EVIPGPDFPT AGQILGRSGI RKAYESGRGS ITIRAKAEIE 
       260        270        280        290        300
QTSSGKERII VTELPYQVNK AKLIEKIADL VRDKKIEGIT DLRDESDRTG 
       310        320        330        340        350
MRIVIEIRRD ANANVILNNL YKQTALQTSF GINLLALVDG QPKVLTLKQC 
       360        370        380        390        400
LEHYLDHQKV VIRRRTAYEL RKAEARAHIL EGLRVALDHL DAVISLIRNS 
       410        420        430        440        450
QTAEIARTGL IEQFSLTEKQ AQAILDMRLQ RLTGLEREKI EEEYQSLVKL 
       460        470        480        490        500
IAELKDILAN EYKVLEIIRE ELTEIKERFN DERRTEIVTS GLETIEDEDL 
       510        520        530        540        550
IERENIVVTL THNGYVKRLP ASTYRSQKRG GKGVQGMGTN EDDFVEHLIS 
       560        570        580        590        600
TSTHDTILFF SNKGKVYRAK GYEIPEYGRT AKGIPIINLL EVEKGEWINA 
       610        620        630        640        650
IIPVTEFNAE LYLFFTTKHG VSKRTSLSQF ANIRNNGLIA LSLREDDELM 
       660        670        680        690        700
GVRLTDGTKQ IIIGTKNGLL IRFPETDVRE MGRTAAGVKG ITLTDDDVVV 
       710        720        730        740        750
GMEILEEESH VLIVTEKGYG KRTPAEEYRT QSRGGKGLKT AKITENNGQL 
       760        770        780        790        800
VAVKATKGEE DLMIITASGV LIRMDINDIS ITGRVTQGVR LIRMAEEEHV 
       810        820 
ATVALVEKNE EDENEEEQEE V
Length:821
Mass (Da):92,099
Last modified:November 1, 1988 - 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:i717847A5F35FB857
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
X02369 Genomic DNA Translation: CAA26222.1
D26185 Genomic DNA Translation: BAA05243.1
AL009126 Genomic DNA Translation: CAB11783.1

Protein sequence database of the Protein Information Resource

More...PIRi		F22930

NCBI Reference Sequences

More...RefSeqi		NP_387888.1, NC_000964.3
WP_003244540.1, NZ_JNCM01000034.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB11783; CAB11783; BSU00070

Database of genes from NCBI RefSeq genomes

More...GeneIDi		940002

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU00070

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.7

<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
X02369 Genomic DNA Translation: CAA26222.1
D26185 Genomic DNA Translation: BAA05243.1
AL009126 Genomic DNA Translation: CAB11783.1
PIRiF22930
RefSeqiNP_387888.1, NC_000964.3
WP_003244540.1, NZ_JNCM01000034.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4DDQX-ray3.30A/B/C/D/E/F1-502[»]
ProteinModelPortaliP05653
SMRiP05653
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP05653, 5 interactors
MINTiP05653
STRINGi224308.Bsubs1_010100000035

Chemistry databases

BindingDBiP05653
DrugBankiDB00537 Ciprofloxacin

Proteomic databases

jPOSTiP05653
PaxDbiP05653
PRIDEiP05653

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB11783; CAB11783; BSU00070
GeneIDi940002
KEGGibsu:BSU00070
PATRICifig|224308.179.peg.7

Phylogenomic databases

eggNOGiENOG4105C24 Bacteria
COG0188 LUCA
HOGENOMiHOG000076278
InParanoidiP05653
KOiK02469
OMAiTHHWLLF
PhylomeDBiP05653

Enzyme and pathway databases

BioCyciBSUB:BSU00070-MONOMER

Family and domain databases

CDDicd00187 TOP4c, 1 hit
Gene3Di1.10.268.10, 1 hit
2.120.10.90, 1 hit
3.90.199.10, 1 hit
HAMAPiMF_01897 GyrA, 1 hit
InterProiView protein in InterPro
IPR005743 GyrA
IPR006691 GyrA/parC_rep
IPR035516 Gyrase/topoIV_suA_C
IPR013760 Topo_IIA-like_dom_sf
IPR002205 Topo_IIA_A/C
IPR013758 Topo_IIA_A/C_ab
IPR013757 Topo_IIA_A_a_sf
PfamiView protein in Pfam
PF03989 DNA_gyraseA_C, 6 hits
PF00521 DNA_topoisoIV, 1 hit
SMARTiView protein in SMART
SM00434 TOP4c, 1 hit
SUPFAMiSSF101904 SSF101904, 1 hit
SSF56719 SSF56719, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		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 nameiGYRA_BACSU
<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: P05653
<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 1, 1988
Last sequence update: November 1, 1988
Last modified: January 16, 2019
This is version 144 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
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