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P0AES4 (GYRA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA gyrase subunit A

EC=5.99.1.3
Gene names
Name:gyrA
Synonyms:hisW, nalA, parD
Ordered Locus Names:b2231, JW2225
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length875 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Ref.11 Ref.12 Ref.14

Catalytic activity

ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.11 Ref.12 Ref.14 Ref.21

Subunit structure

Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis. Can form a 2:2 complex with toxin CcdB in which GyrA is inactive; rejuvenation of GyrA2CcdB2 is effected by CcdA. Ref.11 Ref.12 Ref.14 Ref.20

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_01897.

Miscellaneous

When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA. This enzyme-DNA intermediate is the target of a number of topoisomerase poisons, including toxin CcdB.

Sequence similarities

Belongs to the topoisomerase GyrA/ParC subunit family.

Ontologies

Keywords
   Biological processAntibiotic resistance
   Cellular componentCytoplasm
   LigandATP-binding
DNA-binding
Nucleotide-binding
   Molecular functionIsomerase
Topoisomerase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processATP catabolic process

Inferred from direct assay PubMed 186775PubMed 368801PubMed 6094559. Source: GOC

DNA topological change

Inferred from mutant phenotype PubMed 6327603. Source: EcoliWiki

DNA-dependent DNA replication

Inferred from electronic annotation. Source: UniProtKB-HAMAP

chromosome segregation

Inferred from Biological aspect of Ancestor. Source: RefGenome

response to antibiotic

Inferred from electronic annotation. Source: UniProtKB-KW

response to drug

Inferred from mutant phenotype PubMed 4208771PubMed 6178722PubMed 770163. Source: EcoliWiki

transcription, DNA-templated

Inferred from direct assay PubMed 347446. Source: EcoliWiki

   Cellular_componentchromosome

Inferred from electronic annotation. Source: InterPro

cytoplasm

Inferred from direct assay PubMed 16858726. Source: UniProtKB

membrane

Inferred from direct assay PubMed 16858726. Source: UniProtKB

nucleoid

Inferred from Biological aspect of Ancestor. Source: RefGenome

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

DNA binding

Inferred from direct assay PubMed 1851291PubMed 6294616. Source: EcoliWiki

DNA topoisomerase type II (ATP-hydrolyzing) activity

Inferred from direct assay PubMed 186775. Source: CACAO

DNA-dependent ATPase activity

Inferred from direct assay PubMed 6094559. Source: EcoliWiki

identical protein binding

Inferred from physical interaction PubMed 16858726PubMed 19834901. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed HAMAP-Rule MF_01897
Chain2 – 875874DNA gyrase subunit A HAMAP-Rule MF_01897
PRO_0000145232

Sites

Active site1221O-(5'-phospho-DNA)-tyrosine intermediate Ref.9

Natural variations

Natural variant671A → S in PPA-10; quinolone-resistant.
Natural variant811G → C in NAL-97; quinolone-resistant.
Natural variant831S → L in NAL-51, NAL-112, NAL-118 and NAL-119; quinolone-resistant.
Natural variant831S → W in PPA-18 and strain 227; quinolone-resistant.
Natural variant841A → P in PPA-05; quinolone-resistant.
Natural variant871D → N in NAL-113 and KL-16; quinolone-resistant.
Natural variant871D → V in strain: 202; quinolone-resistant.
Natural variant1061Q → H in NAL-89; quinolone-resistant.
Natural variant6781D → E in strain: 227.
Natural variant7981I → IMMI in KL-16; quinolone-resistant.
Natural variant8281A → S in strain: 227.

Experimental info

Mutagenesis321R → A or Q: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and relaxation. Ref.11
Mutagenesis471R → Q: Nearly abolishes DNA supercoiling. Reduces DNA cleavage. Slightly reduces DNA relaxation. Ref.11
Mutagenesis781H → A: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and DNA relaxation. Ref.11
Mutagenesis801H → A: Reduces DNA supercoiling. Slightly reduces DNA cleavage. No effect on DNA relaxation. Ref.11
Mutagenesis831S → A: Resistant to fluoroquinolones. Ref.17
Mutagenesis1061Q → R: Resistant to fluoroquinolones. Ref.17
Mutagenesis4621R → 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. Ref.18 Ref.19

Secondary structure

........................................................................................................................................ 875
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0AES4 [UniParc].

Last modified December 20, 2005. Version 1.
Checksum: 3FD5BD52A5969069

FASTA87596,964
        10         20         30         40         50         60 
MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN 

        70         80         90        100        110        120 
KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM 

       130        140        150        160        170        180 
RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT 

       190        200        210        220        230        240 
NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV 

       250        260        270        280        290        300 
YIRARAEVEV DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG 

       310        320        330        340        350        360 
MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI IAAFVRHRRE 

       370        380        390        400        410        420 
VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA PTPAEAKTAL VANPWQLGNV 

       430        440        450        460        470        480 
AAMLERAGDD AARPEWLEPE FGVRDGLYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE 

       490        500        510        520        530        540 
LLDQIAELLR ILGSADRLME VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV 

       550        560        570        580        590        600 
VTLSHQGYVK YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY 

       610        620        630        640        650        660 
SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT ANGTVKKTVL 

       670        680        690        700        710        720 
TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE GKVVRFKESS VRAMGCNTTG 

       730        740        750        760        770        780 
VRGIRLGEGD KVVSLIVPRG DGAILTATQN GYGKRTAVAE YPTKSRATKG VISIKVTERN 

       790        800        810        820        830        840 
GLVVGAVQVD DCDQIMMITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA 

       850        860        870 
EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEE 

« Hide

References

« Hide 'large scale' references
[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].
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].
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. expand/collapse author list , 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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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: ACTIVE SITE TYR-122.
[10]"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.
[11]"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.
[12]"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: CATALYTIC ACTIVITY, FUNCTION, COFACTOR, SUBUNIT.
[13]"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.
[14]"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 2-523 IN COMPLEX WITH ANTIBIOTIC SIMOCYCLINONE D8, CATALYTIC ACTIVITY, SUBUNIT, FUNCTION.
[15]"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.
[16]"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.
[17]"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.
[18]"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.
[19]"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.
[20]"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.
[21]"Crystal structure of the breakage-reunion domain of DNA gyrase."
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.
[22]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRITECAP. S02340.
RefSeqNP_416734.1. NC_000913.3.
YP_490470.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP0AES4.
SMRP0AES4. Positions 13-522, 535-841.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36179N.
IntActP0AES4. 51 interactions.
MINTMINT-201682.
STRING511145.b2231.

Chemistry

BindingDBP0AES4.
ChEMBLCHEMBL1858.

2D gel databases

SWISS-2DPAGEP0AES4.

Proteomic databases

PaxDbP0AES4.
PRIDEP0AES4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75291; AAC75291; b2231.
BAA16048; BAA16048; BAA16048.
GeneID12933138.
946614.
KEGGecj:Y75_p2193.
eco:b2231.
PATRIC32119821. VBIEscCol129921_2320.

Organism-specific databases

EchoBASEEB0418.
EcoGeneEG10423. gyrA.

Phylogenomic databases

eggNOGCOG0188.
HOGENOMHOG000076278.
KOK02469.
OMAETVDWVP.
OrthoDBEOG661H5V.
ProtClustDBPRK05560.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0AES4.

Family and domain databases

Gene3D1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.
HAMAPMF_01897. GyrA.
InterProIPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
IPR013760. Topo_IIA_like_dom.
[Graphical view]
PfamPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMSSF56719. SSF56719. 1 hit.
TIGRFAMsTIGR01063. gyrA. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0AES4.
PROP0AES4.

Entry information

Entry nameGYRA_ECOLI
AccessionPrimary (citable) accession number: P0AES4
Secondary accession number(s): P09097
Entry history
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: April 16, 2014
This is version 85 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene