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Protein

DNA gyrase subunit A

Gene

gyrA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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.

Catalytic activityi

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

Enzyme 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei122 – 1221O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1 Publication

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • 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

  • chromosome segregation Source: GO_Central
  • DNA-dependent DNA replication Source: UniProtKB-HAMAP
  • DNA topological change Source: EcoliWiki
  • response to antibiotic Source: UniProtKB-KW
  • response to drug Source: EcoliWiki
  • transcription, DNA-templated Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10423-MONOMER.
ECOL316407:JW2225-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10423. gyrA.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • chromosome Source: InterPro
  • cytoplasm Source: UniProtKB
  • cytosol Source: EcoCyc
  • membrane Source: UniProtKB
  • nucleoid Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi32 – 321R → A or Q: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and relaxation. 1 Publication
Mutagenesisi47 – 471R → Q: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage. Slightly reduces DNA relaxation. 1 Publication
Mutagenesisi78 – 781H → A: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and DNA relaxation. 1 Publication
Mutagenesisi80 – 801H → A: Reduces DNA supercoiling. Slightly reduces quinolone-induced DNA cleavage. No effect on DNA relaxation. 1 Publication
Mutagenesisi83 – 831S → A: Resistant to fluoroquinolones. 1 Publication
Mutagenesisi106 – 1061Q → R: Resistant to fluoroquinolones. 1 Publication
Mutagenesisi462 – 4621R → 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 Publications
Mutagenesisi560 – 5667QRRGGKG → 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 Publication
Mutagenesisi560 – 5667Missing : Loss of gyrase-mediated DNA wrapping, nearly complete loss of DNA supercoiling activity, no change in DNA supercoil relaxation or DNA decatenation activity. 1 Publication
Mutagenesisi842 – 85615Missing : 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
BLAST
Mutagenesisi854 – 87522Missing : Isolated CTD gains ability to wrap DNA around itself in the absence of GyrB, binds DNA better than wild-type CTD. 1 PublicationAdd
BLAST

Chemistry

ChEMBLiCHEMBL2311224.
DrugBankiDB00537. Ciprofloxacin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 875874DNA gyrase subunit APRO_0000145232Add
BLAST

Proteomic databases

EPDiP0AES4.
PaxDbiP0AES4.
PRIDEiP0AES4.

2D gel databases

SWISS-2DPAGEP0AES4.

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

WithEntry#Exp.IntActNotes
itself2EBI-547129,EBI-547129
gyrBP0AES65EBI-547129,EBI-541911
marRP272452EBI-547129,EBI-6409744

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4262132. 260 interactions.
DIPiDIP-36179N.
IntActiP0AES4. 52 interactions.
MINTiMINT-201682.
STRINGi511145.b2231.

Chemistry

BindingDBiP0AES4.

Structurei

Secondary structure

1
875
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni31 – 333Combined sources
Turni37 – 393Combined sources
Helixi43 – 5412Combined sources
Beta strandi59 – 613Combined sources
Helixi66 – 7611Combined sources
Helixi82 – 9110Combined sources
Turni95 – 973Combined sources
Beta strandi102 – 1076Combined sources
Turni120 – 1223Combined sources
Beta strandi124 – 1274Combined sources
Helixi131 – 1344Combined sources
Turni136 – 1416Combined sources
Beta strandi145 – 1473Combined sources
Beta strandi151 – 1588Combined sources
Helixi165 – 1695Combined sources
Beta strandi171 – 1733Combined sources
Beta strandi180 – 1823Combined sources
Helixi187 – 19913Combined sources
Helixi205 – 2084Combined sources
Turni209 – 2113Combined sources
Helixi227 – 2359Combined sources
Beta strandi236 – 2438Combined sources
Beta strandi245 – 2495Combined sources
Beta strandi258 – 2636Combined sources
Helixi270 – 28112Combined sources
Turni282 – 2843Combined sources
Beta strandi292 – 2943Combined sources
Beta strandi298 – 3003Combined sources
Beta strandi303 – 3053Combined sources
Helixi314 – 32310Combined sources
Beta strandi327 – 3337Combined sources
Beta strandi335 – 3384Combined sources
Beta strandi341 – 3444Combined sources
Helixi347 – 38842Combined sources
Helixi390 – 39910Combined sources
Beta strandi400 – 4023Combined sources
Helixi403 – 41210Combined sources
Helixi419 – 4213Combined sources
Beta strandi441 – 4499Combined sources
Helixi452 – 4598Combined sources
Helixi463 – 4664Combined sources
Helixi468 – 49326Combined sources
Helixi495 – 51319Combined sources
Beta strandi519 – 5213Combined sources
Beta strandi538 – 5447Combined sources
Beta strandi547 – 5537Combined sources
Helixi556 – 5605Combined sources
Beta strandi578 – 5858Combined sources
Beta strandi589 – 5946Combined sources
Beta strandi597 – 6037Combined sources
Helixi604 – 6063Combined sources
Beta strandi612 – 6143Combined sources
Helixi619 – 6213Combined sources
Beta strandi631 – 6388Combined sources
Beta strandi645 – 6506Combined sources
Beta strandi653 – 6597Combined sources
Helixi660 – 6634Combined sources
Beta strandi671 – 6744Combined sources
Beta strandi682 – 6887Combined sources
Beta strandi693 – 6986Combined sources
Beta strandi701 – 7077Combined sources
Helixi708 – 7103Combined sources
Beta strandi732 – 7365Combined sources
Beta strandi743 – 7486Combined sources
Beta strandi751 – 7566Combined sources
Helixi758 – 7603Combined sources
Beta strandi771 – 7744Combined sources
Turni778 – 7803Combined sources
Beta strandi782 – 7898Combined sources
Beta strandi794 – 8018Combined sources
Beta strandi804 – 8085Combined sources
Helixi809 – 8113Combined sources
Beta strandi833 – 8386Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 13-522, 535-841.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AES4.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni531 – 841311C-terminal domain (CTD)1 PublicationAdd
BLAST
Regioni842 – 87534Acidic tail1 PublicationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi560 – 5667GyrA-box1 PublicationUniRule annotation

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.
OMAiETVDWVP.
OrthoDBiEOG661H5V.
PhylomeDBiP0AES4.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.
HAMAPiMF_01897. GyrA.
InterProiIPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR013760. Topo_IIA-like_dom.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
[Graphical view]
PfamiPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTiSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01063. gyrA. 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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti67 – 671A → S in PPA-10; quinolone-resistant. 1 Publication
Natural varianti81 – 811G → C in NAL-97; quinolone-resistant. 1 Publication
Natural varianti83 – 831S → L in NAL-51, NAL-112, NAL-118, NAL-119 and strains 58, 158, 218, 231 and 235; quinolone-resistant. 2 Publications
Natural varianti83 – 831S → W in PPA-18 and strains 233 and 227; quinolone-resistant. 3 Publications
Natural varianti84 – 841A → P in PPA-05; quinolone-resistant. 1 Publication
Natural varianti87 – 871D → N in NAL-113 and OV6; quinolone-resistant. 2 Publications
Natural varianti87 – 871D → V in strain: 202; partially quinolone-resistant. 1 Publication
Natural varianti106 – 1061Q → H in NAL-89; quinolone-resistant. 1 Publication
Natural varianti678 – 6781D → E in strain: 227. 1 Publication
Natural varianti798 – 7981I → IMMI in strain OV6; quinolone-resistant. 1 Publication
Natural varianti828 – 8281A → S in strain: 227. 1 Publication

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.
PATRICi32119821. VBIEscCol129921_2320.

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
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. Positions 13-522, 535-841.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262132. 260 interactions.
DIPiDIP-36179N.
IntActiP0AES4. 52 interactions.
MINTiMINT-201682.
STRINGi511145.b2231.

Chemistry

BindingDBiP0AES4.
ChEMBLiCHEMBL2311224.
DrugBankiDB00537. Ciprofloxacin.

2D gel databases

SWISS-2DPAGEP0AES4.

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.
PATRICi32119821. VBIEscCol129921_2320.

Organism-specific databases

EchoBASEiEB0418.
EcoGeneiEG10423. gyrA.

Phylogenomic databases

eggNOGiENOG4105C24. Bacteria.
COG0188. LUCA.
HOGENOMiHOG000076278.
InParanoidiP0AES4.
KOiK02469.
OMAiETVDWVP.
OrthoDBiEOG661H5V.
PhylomeDBiP0AES4.

Enzyme and pathway databases

BioCyciEcoCyc:EG10423-MONOMER.
ECOL316407:JW2225-MONOMER.
MetaCyc:EG10423-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AES4.
PROiP0AES4.

Family and domain databases

Gene3Di1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.
HAMAPiMF_01897. GyrA.
InterProiIPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR013760. Topo_IIA-like_dom.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
[Graphical view]
PfamiPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTiSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01063. gyrA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase."
    Swanberg S.L., Wang J.C.
    J. Mol. Biol. 197:729-736(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Quinolone-resistant mutations of the gyrA gene of Escherichia coli."
    Yoshida H., Kojima T., Yamagishi J., Nakamura S.
    Mol. Gen. Genet. 211:1-7(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / KL16.
  3. "The parD- mutant of Escherichia coli also carries a gyrAam mutation. The complete sequence of gyrA."
    Hussain K., Elliott E.J., Salmond G.P.C.
    Mol. Microbiol. 1:259-273(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS QUINOLONE-RESISTANTS ASN-87 AND ILE-MET-MET-ILE-798.
    Strain: OV6.
  4. "Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones."
    Cullen M.E., Wyke A.W., Kuroda R., Fisher L.M.
    Antimicrob. Agents Chemother. 33:886-894(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS QUINOLONE-RESISTANT GLU-678 AND SER-828.
    Strain: 227.
  5. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  7. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  8. "Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment."
    Menzel R., Gellert M.
    J. Bacteriol. 169:1272-1278(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-88, PARTIAL PROTEIN SEQUENCE.
  9. "Mapping the active site tyrosine of Escherichia coli DNA gyrase."
    Horowitz D.S., Wang J.C.
    J. Biol. Chem. 262:5339-5344(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 17-24; 61-66 AND 123-126, FUNCTION, ACTIVE SITE, REACTION MECHANISM, DNA-BINDING.
  10. "DNA gyrase: an enzyme that introduces superhelical turns into DNA."
    Gellert M., Mizuuchi K., O'Dea M.H., Nash H.A.
    Proc. Natl. Acad. Sci. U.S.A. 73:3872-3876(1976) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN GENERATING NEGATIVELY SUPERCOILED DNA, CATALYTIC ACTIVITY, ATP-DEPENDENCE.
  11. "Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity."
    Gellert M., Mizuuchi K., O'Dea M.H., Itoh T., Tomizawa J.I.
    Proc. Natl. Acad. Sci. U.S.A. 74:4772-4776(1977) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN RELAXING SUPERCOILED DNA, ENZYME REGULATION.
  12. "Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli."
    Yoshida H., Bogaki M., Nakamura M., Nakamura S.
    Antimicrob. Agents Chemother. 34:1271-1272(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS QUINOLONE-RESISTANT SER-67; CYS-81; LEU-83; TRP-83; PRO-84; ASN-87 AND HIS-106.
    Strain: K12 / KL16.
  13. "4-quinolone resistance mutations in the DNA gyrase of Escherichia coli clinical isolates identified by using the polymerase chain reaction."
    Oram M., Fisher L.M.
    Antimicrob. Agents Chemother. 35:387-389(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS QUINOLONE-RESISTANT LEU-83; TRP-83 AND VAL-87.
  14. "Novel quinolone resistance mutations of the Escherichia coli DNA gyrase A protein: enzymatic analysis of the mutant proteins."
    Hallett P., Maxwell A.
    Antimicrob. Agents Chemother. 35:335-340(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF SER-83 AND GLN-106.
    Strain: K12.
  15. "Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes."
    Bernard P., Couturier M.
    J. Mol. Biol. 226:735-745(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: INHIBITION BY TOXIN PROTEIN CCDB, MUTAGENESIS OF ARG-462.
    Strain: K12.
  16. "The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase."
    Bernard P., Kezdy K.E., Van Melderen L., Steyaert J., Wyns L., Pato M.L., Higgins P.N., Couturier M.
    J. Mol. Biol. 234:534-541(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-462.
  17. "Mechanism of inhibition of DNA gyrase by cyclothialidine, a novel DNA gyrase inhibitor."
    Nakada N., Gmuender H., Hirata T., Arisawa M.
    Antimicrob. Agents Chemother. 38:1966-1973(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  18. "Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA)."
    Maki S., Takiguchi S., Horiuchi T., Sekimizu K., Miki T.
    J. Mol. Biol. 256:473-482(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: INHIBITION BY TOXIN PROTEIN CCDB, REJUVENATION BY CCDA, SUBUNIT.
  19. "Conversion of DNA gyrase into a conventional type II topoisomerase."
    Kampranis S.C., Maxwell A.
    Proc. Natl. Acad. Sci. U.S.A. 93:14416-14421(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN.
  20. "acrB mutation located at carboxyl-terminal region of gyrase B subunit reduces DNA binding of DNA gyrase."
    Funatsuki K., Tanaka R., Inagaki S., Konno H., Katoh K., Nakamura H.
    J. Biol. Chem. 272:13302-13308(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION, SUBUNIT, DNA-BINDING.
    Strain: K12 / N2879.
  21. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  22. "Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli."
    Zechiedrich E.L., Khodursky A.B., Cozzarelli N.R.
    Genes Dev. 11:2580-2592(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  23. "Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus."
    Ward D.V., Newton A.
    Mol. Microbiol. 26:897-910(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION AND DISCUSSION OF GYRA-BOX, DOMAIN.
  24. "Identification of four GyrA residues involved in the DNA breakage-reunion reaction of DNA gyrase."
    Hockings S.C., Maxwell A.
    J. Mol. Biol. 318:351-359(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ARG-32; ARG-47; HIS-78 AND HIS-80.
  25. "The 'GyrA-box' is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction."
    Kramlinger V.M., Hiasa H.
    J. Biol. Chem. 281:3738-3742(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF 560-GLN--GLY-566.
  26. "Growth rate toxicity phenotypes and homeostatic supercoil control differentiate Escherichia coli from Salmonella enterica serovar Typhimurium."
    Champion K., Higgins N.P.
    J. Bacteriol. 189:5839-5849(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  27. "DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action."
    Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A., Palumbo M.
    Biochemistry 47:8538-8545(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
  28. "The pentapeptide repeat proteins MfpAMt and QnrB4 exhibit opposite effects on DNA gyrase catalytic reactions and on the ternary gyrase-DNA-quinolone complex."
    Merens A., Matrat S., Aubry A., Lascols C., Jarlier V., Soussy C.J., Cavallo J.D., Cambau E.
    J. Bacteriol. 191:1587-1594(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  29. Cited for: FUNCTION, ENZYME REGULATION.
  30. "Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity."
    Tretter E.M., Berger J.M.
    J. Biol. Chem. 287:18636-18644(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN, DNA-BINDING, MUTAGENESIS OF 842-PRO--ALA-856 AND 854-SER--GLU-875.
  31. "Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency."
    Tretter E.M., Berger J.M.
    J. Biol. Chem. 287:18645-18654(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DNA-BINDING, MUTAGENESIS OF 842-PRO--ALA-856.
  32. "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE), Part II: development of inhibitors with broad spectrum, Gram-negative antibacterial activity."
    Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J., Creighton C.J., Cunningham M.L., Kwan B., Stidham M., Nelson K., Brown-Driver V., Castellano A., Shaw K.J., Lightstone F.C., Wong S.E., Nguyen T.B., Finn J., Tari L.W.
    Bioorg. Med. Chem. Lett. 23:1537-1543(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  33. "Crystal structure of the breakage-reunion domain of DNA gyrase."
    Morais Cabral J.H., Jackson A.P., Smith C.V., Shikotra N., Maxwell A., Liddington R.C.
    Nature 388:903-906(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522, CATALYTIC ACTIVITY.
  34. "Molecular basis of gyrase poisoning by the addiction toxin CcdB."
    Dao-Thi M.H., Van Melderen L., De Genst E., Afif H., Buts L., Wyns L., Loris R.
    J. Mol. Biol. 348:1091-1102(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 363-494 IN COMPLEX WITH CCBD, SUBUNIT.
  35. "A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias."
    Ruthenburg A.J., Graybosch D.M., Huetsch J.C., Verdine G.L.
    J. Biol. Chem. 280:26177-26184(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 535-841, DOMAIN.
    Strain: K12.
  36. "A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase."
    Edwards M.J., Flatman R.H., Mitchenall L.A., Stevenson C.E., Le T.B., Clarke T.A., McKay A.R., Fiedler H.P., Buttner M.J., Lawson D.M., Maxwell A.
    Science 326:1415-1418(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.62 ANGSTROMS) OF 1-525 IN COMPLEX WITH ANTIBIOTIC, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.

Entry informationi

Entry nameiGYRA_ECOLI
AccessioniPrimary (citable) accession number: P0AES4
Secondary accession number(s): P09097
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: April 13, 2016
This is version 105 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.