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gyrA:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

GyrA

Synonyms

DNA gyrase (type II topoisomerase), subunit A[1], B2231[2][1], ParD[2][1], NorA[2][1], NfxA[2][1], NalA[2][1], HisW[2][1], GyrA[2][1]

Product description

DNA gyrase, subunit A[2][3];

Component of DNA gyrase[3]

DNA gyrase, subunit A; nalidixic acid resistance; cold shock regulon[4]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR002205
InterPro:IPR005743
InterPro:IPR006691
InterPro:IPR013757
InterPro:IPR013758
InterPro:IPR013760
SP_KW:KW-0238

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0003916

DNA topoisomerase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006691
SP_KW:KW-0799

F

Seeded from EcoCyc [6]

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR002205
InterPro:IPR005743
InterPro:IPR013757
InterPro:IPR013758
InterPro:IPR013760
EC:5.99.1.3

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002205
InterPro:IPR005743
InterPro:IPR006691
InterPro:IPR013757
InterPro:IPR013758
InterPro:IPR013760

F

Seeded from EcoCyc [6]

complete

GO:0005694

chromosome

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002205
InterPro:IPR005743
InterPro:IPR006691
InterPro:IPR013757
InterPro:IPR013758
InterPro:IPR013760

C

Seeded from EcoCyc [6]

complete

GO:0006265

DNA topological change

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002205
InterPro:IPR005743
InterPro:IPR006691
InterPro:IPR013757
InterPro:IPR013758
InterPro:IPR013760

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0006268

DNA unwinding during replication

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005743
InterPro:IPR006691

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0016853

isomerase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc [6]

complete

GO:0046677

response to antibiotic

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc [6]

complete

GO:0005624

membrane fraction

PMID:16858726[7]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [6]

complete

GO:0005737

cytoplasm

PMID:16858726[7]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [6]

complete

GO:0005739

mitochondrion

PMID:16858726[7]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [6]

complete

GO:0006261

DNA-dependent DNA replication

PMID:227840[8]

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc 11.1[3].

gyrA(ts)

complete

GO:0042493

response to drug

PMID:6178722[9]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0003918

DNA topoisomerase (ATP-hydrolyzing) activity

PMID:368801[10]

IDA: Inferred from Direct Assay

F

With GyrB

Purified E. coli gyrase was shown to induce cleavage and supercoiling in ColE1 DNA in the presence of ATP, but not after the addition of novobiocin or coumermycin A1 (Figure 2). Supercoiling of DNA was monitored by agarose gel electrophoresis (Figure 2A), while the hydrolysis of ATP was measured by following the release of 32-Pi measured by thin layer chromatography (Figure 2B).

complete

GO:0003677

DNA binding

PMID:6294616[11]

IDA: Inferred from Direct Assay

F

E. coli gyrase incubated with radiolabeled ColE1 DNA and passed over nitrocellulose filters. The complexes were retained on the filters and radioactivity of the filters was measured and reported in Figure 1.

complete

GO:0042493

response to drug

PMID:770163[12]

IMP: Inferred from Mutant Phenotype

P

Oxolinic acid (Quinolone)

complete

GO:0042493

response to drug

PMID:4208771[13]

IMP: Inferred from Mutant Phenotype

P

Naladixic Acid (Quinolone)

complete

GO:0003677

DNA binding

PMID:1851291[14]

IDA: Inferred from Direct Assay

F

The C-terminal domain of GyrA (572-857aa) was shown to bind and retard the movement of a 147bp fragment of ColE1 DNA through a 5% polyacrylamide gel (Figure 2).

complete

GO:0009330

DNA topoisomerase complex (ATP-hydrolyzing)

PMID:347446[15]

IDA: Inferred from Direct Assay

C

E. coli gyrase consists of the gene products of gyrA and gyrB genes (Figures 2 & 7).

complete

GO:0008094

DNA-dependent ATPase activity

PMID:6094559[16]

IDA: Inferred from Direct Assay

F

GyrA and DNA (bound to GyrA) are required for ATPase activity of GyrB (Figure 1).

complete

GO:0006265

DNA topological change

PMID:6327603[17]

IMP: Inferred from Mutant Phenotype

P

Nucleoids from E. coli cells containing DNA labeled with [methyl-3H]thymidine were isolated and separated using an ethidium bromide-containing sucrose density gradient. The sedimentation profiles were reported for gyrA and gyrB temperature-sensitive mutants at the permissive and non-permissive temperatures (Figure 1 & 2). The ethidium bromide concentration is proportional to superhelical density, meaning that less supercoiled DNA from a gyrase mutant grown at the non-permissive temperature requires a lower concentration of ethidium bromide.

complete

GO:0006350

transcription

PMID:15535863[18]

IMP: Inferred from Mutant Phenotype

P

The authors used 3 conditions (treatment with either a quinolone or coumarin anitbiotic or growth of a gyrAts mutant at non-permissive temperature) to alter negative supercoiling of DNA and measured the changes in gene expression by microarray analysis. More than 300 SSGs (supercoiling sensitive genes) were identified that responded rapidly to the experimental conditions.

complete

GO:0005737

cytoplasm

PMID:7952188[19]

IDA: Inferred from Direct Assay

C

Immunogold labeling of cells with anti-GyrA antibodies indicated the presence of GyrA in the cytoplasm of E. coli.

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

Subunits of DNA gyrase

could be indirect

Protein

ycgC

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

aceF

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

add

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

clpA

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

dnaJ

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

dnaK

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

ffh

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

ftsZ

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

glyS

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

zraS

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

lpdA

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

malK

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

metK

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

pstB

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

recA

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

rho

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

rpsB

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

tufA

PMID:15690043[20]

Experiment(s):EBI-884206, EBI-891237

Protein

yjfZ

PMID:15690043[20]

Experiment(s):EBI-884206

Protein

argS

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

idnO

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

rpsB

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

yfaS

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

aspC

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

nrdI

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

rtcB

PMID:16606699[21]

Experiment(s):EBI-1142253

Protein

GyrB

The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Higgins & Cozzarelli (1982)[11]
Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. Higgins et al. (1978) [15]

Small Molecule

Naladixic Acid

Studies on the mechanism of action of nalidixic acid. Bourguignon et al. (1973) [13]

Small Molecule

Oxolinic acid

Replication of Escherichia coli DNA in vitro: inhibition by oxolinic acid. Staudenbauer (1976) [12]

DNA

DNA

The C-terminal domain of GyrA is sufficient to bind DNA (residues 572-875).

The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Reece & Maxwell (1991) [14]


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN
KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM
RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT
NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV
YIRARAEVEV DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG
MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI IAAFVRHRRE
VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA PTPAEAKTAL VANPWQLGNV
AAMLERAGDD AARPEWLEPE FGVRDGLYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE
LLDQIAELLR ILGSADRLME VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV
VTLSHQGYVK YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY
SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT ANGTVKKTVL
TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE GKVVRFKESS VRAMGCNTTG
VRGIRLGEGD KVVSLIVPRG DGAILTATQN GYGKRTAVAE YPTKSRATKG VISIKVTERN
GLVVGAVQVD DCDQIMMITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA
EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEE
Length

875

Mol. Wt

96.964 kDa

pI

5.0 (calculated)

Extinction coefficient

52,260 - 52,760 (calc based on 24 Y, 3 W, and 4 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

TypeResiduesDescriptionNotesReferences
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rectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglerectanglemotifs

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10423-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P0AES4

UniProt (EcoliWiki Page)

UniProt:P0AES4

PFAM (EcoliWiki Page)

PFAM:PF00521

RefSeq (EcoliWiki Page)

RefSeq:NP_416734


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 5.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  6. ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  7. ↑ 7.0 7.1 7.2 Lasserre JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27: 3306-21 PubMed EcoliWiki page
  8. ↑ Kreuzer KN & Cozzarelli NR (1979) Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription, and bacteriophage growth. J Bacteriol 140: 424-35 PubMed EcoliWiki page
  9. ↑ Chao L & Tillman DM (1982) Enhanced resistance to nitrosoguanidine killing and mutagenesis in a DNA gyrase mutant of Escherichia coli. J Bacteriol 151: 764-70 PubMed EcoliWiki page
  10. ↑ Sugino A et al. (1978) Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc Natl Acad Sci U S A 75: 4838-42 PubMed EcoliWiki page
  11. ↑ 11.0 11.1 Higgins NP & Cozzarelli NR (1982) The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Nucleic Acids Res 10: 6833-47 PubMed EcoliWiki page
  12. ↑ 12.0 12.1 Staudenbauer WL (1976) Replication of Escherichia coli DNA in vitro: inhibition by oxolinic acid. Eur J Biochem 62: 491-7 PubMed EcoliWiki page
  13. ↑ 13.0 13.1 Bourguignon GJ et al. (1973) Studies on the mechanism of action of nalidixic acid. Antimicrob Agents Chemother 4: 479-86 PubMed EcoliWiki page
  14. ↑ 14.0 14.1 Reece RJ & Maxwell A (1991) The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Res 19: 1399-405 PubMed EcoliWiki page
  15. ↑ 15.0 15.1 Higgins NP et al. (1978) Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity. Proc Natl Acad Sci U S A 75: 1773-7 PubMed EcoliWiki page
  16. ↑ Maxwell A & Gellert M (1984) The DNA dependence of the ATPase activity of DNA gyrase. J Biol Chem 259: 14472-80 PubMed EcoliWiki page
  17. ↑ Steck TR et al. (1984) DNA supercoiling in gyrase mutants. J Bacteriol 158: 397-403 PubMed EcoliWiki page
  18. ↑ Peter BJ et al. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 5: R87 PubMed EcoliWiki page
  19. ↑ Thornton M et al. (1994) Immunogold localization of GyrA and GyrB proteins in Escherichia coli. Microbiology 140 ( Pt 9): 2371-82 PubMed EcoliWiki page
  20. ↑ 20.00 20.01 20.02 20.03 20.04 20.05 20.06 20.07 20.08 20.09 20.10 20.11 20.12 20.13 20.14 20.15 20.16 20.17 20.18 Butland G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-7 PubMed EcoliWiki page
  21. ↑ 21.0 21.1 21.2 21.3 21.4 21.5 21.6 Arifuzzaman M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686-91 PubMed EcoliWiki page

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