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Protein

DNA gyrase subunit A

Gene

gyrA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to maintain chromosomes in an underwound state (PubMed:3031051, PubMed:186775, PubMed:7811004, PubMed:9148951, PubMed:12051842, PubMed:18642932, PubMed:19060136, PubMed:20356737, PubMed:22457353, PubMed:23294697, PubMed:19965760). This makes better substrates for topoisomerase IV (ParC and ParE) which is the main enzyme that unlinks newly replicated chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes (PubMed:22457352). Relaxes negatively supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli gyrase has higher supercoiling activity than many other bacterial gyrases; at comparable concentrations E.coli gyrase introduces more supercoils faster than M.tuberculosis gyrase, while M.tuberculosis gyrase has higher decatenation than supercoiling activity compared to E.coli (PubMed:22457352). E.coli makes 15% more negative supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed in S.typhimurium even though the 2 subunits have 777/804 residues identical (PubMed:17400739). The enzymatic differences between E.coli gyrase and topoisomerase IV are largely due to the GyrA C-terminal domain (approximately residues 524-841) and specifically the GyrA-box (PubMed:8962066, PubMed:16332690).17 Publications
Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.

Miscellaneous

When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA (PubMed:3031051). In the presence of quinolones this intermediate can be trapped and is used as an indicator of drug toxicity (PubMed:12051842). The enzyme-DNA intermediate is also the target of a number of topoisomerase poisons, including toxin CcdB (PubMed:1324324, PubMed:8254658).1 Publication3 Publications
Few gyrases are as efficient as E.coli at forming negative supercoils (PubMed:22457352, PubMed:17400739). 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 annotation2 Publications

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation5 Publications

Activity regulationi

Gyrase is the target of many classes of inhibitors, including coumarins, cyclothialidines, pyrrolopyrimidines, pyrazolthiazoles and (fluoro)quinolones. Quinolones bind GyrA when the enzyme is complexed with DNA and trap the enzyme in a covalent reaction intermediate with DNA (PubMed:3031051, PubMed:12051842). Coumarins bind to GyrB and are competitive inhibitors of its ATPase activity (PubMed:7811004). Cyclothialidines also bind GyrB and are ATPase competitive inhibitors; they seem to act differently from coumarins (PubMed:7811004). Pyrrolopyrimidines inhibit both GyrB and its paralog in topoisomerase IV (parE) (PubMed:23294697). Pyrazolthiazoles also inhibit the ATPase activity of GyrB (PubMed:20356737). DNA supercoiling and relaxation are both inhibited by oxolinic acid (PubMed:337300). Acriflavine inhibits supercoiling activity and DNA-stimulated ATPase activity (PubMed:9148951). DNA supercoiling activity is protected from fluoroquinolone inhibition by QnrB4; QnrB4 has no effect on supercoiling activity alone (PubMed:19060136).6 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei122O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1 Publication1

GO - Molecular functioni

  • ATP binding Source: GO_Central
  • DNA binding Source: EcoliWiki
  • DNA-dependent ATPase activity Source: EcoliWiki
  • DNA supercoiling activity Source: UniProtKB
  • DNA topoisomerase type II (ATP-hydrolyzing) activity Source: CACAO
  • identical protein binding Source: IntAct

GO - Biological processi

  • DNA-dependent DNA replication Source: UniProtKB-UniRule
  • DNA topological change Source: EcoliWiki
  • response to antibiotic Source: UniProtKB-KW
  • response to drug Source: EcoliWiki
  • transcription, DNA-templated Source: EcoliWiki

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
Biological processAntibiotic resistance
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10423-MONOMER
MetaCyc:EG10423-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit AUniRule annotation (EC:5.99.1.3UniRule annotation5 Publications)
Gene namesi
Name:gyrAUniRule annotation
Synonyms:hisW, nalA1 Publication, parD
Ordered Locus Names:b2231, JW2225
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10423 gyrA

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi32R → A or Q: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and relaxation. 1 Publication1
Mutagenesisi47R → Q: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage. Slightly reduces DNA relaxation. 1 Publication1
Mutagenesisi78H → A: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and DNA relaxation. 1 Publication1
Mutagenesisi80H → A: Reduces DNA supercoiling. Slightly reduces quinolone-induced DNA cleavage. No effect on DNA relaxation. 1 Publication1
Mutagenesisi83S → A: Resistant to fluoroquinolones. 1 Publication1
Mutagenesisi106Q → R: Resistant to fluoroquinolones. 1 Publication1
Mutagenesisi462R → C in gyrA462; resistant to cytotoxic protein CcdB, but not to the quinoline antibiotic enoxacin, has no effect on DNA supercoiling. Does not interact with CcdB. 2 Publications1
Mutagenesisi560 – 566QRRGGKG → AAAAAAA: Loss of gyrase-mediated DNA wrapping, nearly complete loss of DNA supercoiling activity, no change in DNA supercoil relaxation or DNA decatenation activity. 1 Publication7
Mutagenesisi560 – 566Missing : Loss of gyrase-mediated DNA wrapping, nearly complete loss of DNA supercoiling activity, no change in DNA supercoil relaxation or DNA decatenation activity. 1 Publication7
Mutagenesisi842 – 856Missing : Gains ability to wrap DNA around itself in the absence of GyrB; holoenzyme gains ability to wrap DNA in the absence of ATP analogs, but reduces ATP-dependent supercoiling activity 50-fold, DNA is not as extensively negatively supercoiled, has 10-fold less ATP-independent negative supercoiled DNA relaxation activity, no change in ATPase activity of holoenzyme, no change in decatenation ability. Isolated CTD gains ability to wrap DNA around itself in the absence of GyrB, binds DNA better than wild-type CTD. 2 PublicationsAdd BLAST15
Mutagenesisi854 – 875Missing : Isolated CTD gains ability to wrap DNA around itself in the absence of GyrB, binds DNA better than wild-type CTD. 1 PublicationAdd BLAST22

Chemistry databases

ChEMBLiCHEMBL1858
DrugBankiDB00537 Ciprofloxacin

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001452322 – 875DNA gyrase subunit AAdd BLAST874

Proteomic databases

EPDiP0AES4
PaxDbiP0AES4
PRIDEiP0AES4

2D gel databases

SWISS-2DPAGEiP0AES4

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:9148951, PubMed:12051842). In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis (PubMed:12051842, PubMed:18642932, PubMed:19965760, PubMed:9148951). Can form a 2:2 complex with toxin CcdB in which GyrA is inactive; rejuvenation of GyrA2CcdB2 is effected by CcdA (PubMed:15854646, PubMed:1324324, PubMed:8254658, PubMed:8604132).8 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi4262132, 294 interactors
ComplexPortaliCPX-2177 GyrA-GyrB complex
DIPiDIP-36179N
IntActiP0AES4, 53 interactors
MINTiP0AES4
STRINGi316385.ECDH10B_2390

Chemistry databases

BindingDBiP0AES4

Structurei

Secondary structure

1875
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0AES4
SMRiP0AES4
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AES4

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni531 – 841C-terminal domain (CTD)1 PublicationAdd BLAST311
Regioni842 – 875Acidic tail1 PublicationAdd BLAST34

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi560 – 566GyrA-box1 PublicationUniRule annotation7

Domaini

An N-terminal fragment (residues 1-523) can be reconstituted with GyrB, but the complex no longer has negative supercoiling or ATP-independent DNA relaxation activities, although it is capable of DNA cleavage; ATP-dependent relaxation is inhibited by novobiocin and non-hydrolyzable ATP analogs (PubMed:8962066). The fragment has ATP-dependent DNA relaxation and 30-fold improved decatenation activities, unlike holoenzyme it preferentially binds supercoiled DNA (PubMed:8962066). This N-terminal fragment becomes a topoisomerase IV-like enzyme; it poorly complements a temperature-sensitive parC mutation (parC is the topoisomerase IV paralog of gyrA) (PubMed:8962066).1 Publication
The C-terminal domain (CTD, approximately residues 535-841) contains 6 tandemly repeated subdomains known as blades, each of which is composed of a 4-stranded antiparallel beta-sheet (PubMed:15897198). The blades form a circular-shaped beta-pinwheel fold arranged in a spiral around a screw axis, to which DNA probably binds, inducing strong positive superhelicity (about 0.8 links/protein) (PubMed:15897198). The non-conserved, C-terminal acidic tail (residues 842-875) regulates wrapping and DNA-binding by the CTD; deletions within the tail show it is autoinhibitory for DNA wrapping and binding, and couples ATP hydrolysis to DNA strand passage (PubMed:22457353). The GyrA-box is a 7 amino acid motif found in the first blade of the CTD which is discriminative for gyrase versus topoisomerase IV activity (PubMed:9426128). The GyrA-box is required for wrapping of DNA around gyrase, and thus is essential for the DNA supercoiling activity but not DNA relaxation or decatenation activities of gyrase (PubMed:16332690).1 Publication3 Publications

Sequence similaritiesi

Belongs to the type II topoisomerase GyrA/ParC subunit family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C24 Bacteria
COG0188 LUCA
HOGENOMiHOG000076278
InParanoidiP0AES4
KOiK02469
PhylomeDBiP0AES4

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

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AES4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY
60 70 80 90 100
AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY
110 120 130 140 150
MLVDGQGNFG SIDGDSAAAM RYTEIRLAKI AHELMADLEK ETVDFVDNYD
160 170 180 190 200
GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT NIPPHNLTEV INGCLAYIDD
210 220 230 240 250
EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV YIRARAEVEV
260 270 280 290 300
DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG
310 320 330 340 350
MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI
360 370 380 390 400
IAAFVRHRRE VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA
410 420 430 440 450
PTPAEAKTAL VANPWQLGNV AAMLERAGDD AARPEWLEPE FGVRDGLYYL
460 470 480 490 500
TEQQAQAILD LRLQKLTGLE HEKLLDEYKE LLDQIAELLR ILGSADRLME
510 520 530 540 550
VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV VTLSHQGYVK
560 570 580 590 600
YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY
610 620 630 640 650
SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT
660 670 680 690 700
ANGTVKKTVL TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE
710 720 730 740 750
GKVVRFKESS VRAMGCNTTG VRGIRLGEGD KVVSLIVPRG DGAILTATQN
760 770 780 790 800
GYGKRTAVAE YPTKSRATKG VISIKVTERN GLVVGAVQVD DCDQIMMITD
810 820 830 840 850
AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT
860 870
IDGSAAEGDD EIAPEVDVDD EPEEE
Length:875
Mass (Da):96,964
Last modified:December 20, 2005 - v1
Checksum:i3FD5BD52A5969069
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti67A → S in PPA-10; quinolone-resistant. 1 Publication1
Natural varianti81G → C in NAL-97; quinolone-resistant. 1 Publication1
Natural varianti83S → L in NAL-51, NAL-112, NAL-118, NAL-119 and strains 58, 158, 218, 231 and 235; quinolone-resistant. 2 Publications1
Natural varianti83S → W in PPA-18 and strains 233 and 227; quinolone-resistant. 3 Publications1
Natural varianti84A → P in PPA-05; quinolone-resistant. 1 Publication1
Natural varianti87D → N in NAL-113 and OV6; quinolone-resistant. 2 Publications1
Natural varianti87D → V in strain: 202; partially quinolone-resistant. 1 Publication1
Natural varianti106Q → H in NAL-89; quinolone-resistant. 1 Publication1
Natural varianti678D → E in strain: 227. 1 Publication1
Natural varianti798I → IMMI in strain OV6; quinolone-resistant. 1 Publication1
Natural varianti828A → S in strain: 227. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06373 Genomic DNA Translation: CAA29676.1
X06744 Genomic DNA Translation: CAA29919.1
M15631 Genomic DNA Translation: AAA23948.1
U00096 Genomic DNA Translation: AAC75291.1
AP009048 Genomic DNA Translation: BAA16048.1
Y00544 Genomic DNA Translation: CAA68611.1
PIRiS02340 ITECAP
RefSeqiNP_416734.1, NC_000913.3
WP_001281242.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75291; AAC75291; b2231
BAA16048; BAA16048; BAA16048
GeneIDi946614
KEGGiecj:JW2225
eco:b2231
PATRICifig|1411691.4.peg.4

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X06373 Genomic DNA Translation: CAA29676.1
X06744 Genomic DNA Translation: CAA29919.1
M15631 Genomic DNA Translation: AAA23948.1
U00096 Genomic DNA Translation: AAC75291.1
AP009048 Genomic DNA Translation: BAA16048.1
Y00544 Genomic DNA Translation: CAA68611.1
PIRiS02340 ITECAP
RefSeqiNP_416734.1, NC_000913.3
WP_001281242.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AB4X-ray2.80A30-522[»]
1X75X-ray2.80A/B363-494[»]
1ZI0X-ray2.60A/B535-841[»]
2Y3PX-ray2.62A/B2-523[»]
3NUHX-ray3.10A1-525[»]
4ELYX-ray1.93A/B363-497[»]
ProteinModelPortaliP0AES4
SMRiP0AES4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262132, 294 interactors
ComplexPortaliCPX-2177 GyrA-GyrB complex
DIPiDIP-36179N
IntActiP0AES4, 53 interactors
MINTiP0AES4
STRINGi316385.ECDH10B_2390

Chemistry databases

BindingDBiP0AES4
ChEMBLiCHEMBL1858
DrugBankiDB00537 Ciprofloxacin

2D gel databases

SWISS-2DPAGEiP0AES4

Proteomic databases

EPDiP0AES4
PaxDbiP0AES4
PRIDEiP0AES4

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75291; AAC75291; b2231
BAA16048; BAA16048; BAA16048
GeneIDi946614
KEGGiecj:JW2225
eco:b2231
PATRICifig|1411691.4.peg.4

Organism-specific databases

EchoBASEiEB0418
EcoGeneiEG10423 gyrA

Phylogenomic databases

eggNOGiENOG4105C24 Bacteria
COG0188 LUCA
HOGENOMiHOG000076278
InParanoidiP0AES4
KOiK02469
PhylomeDBiP0AES4

Enzyme and pathway databases

BioCyciEcoCyc:EG10423-MONOMER
MetaCyc:EG10423-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AES4
PROiPR:P0AES4

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
ProtoNetiSearch...

Entry informationi

Entry nameiGYRA_ECOLI
AccessioniPrimary (citable) accession number: P0AES4
Secondary accession number(s): P09097
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: November 7, 2018
This is version 130 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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