P9WG47 · GYRA_MYCTU

Function

function

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, while in the absence of ATP it relaxes supercoiled dsDNA (PubMed:15047530, PubMed:16377674, PubMed:16876125, PubMed:17015625, PubMed:18426901, PubMed:19060136, PubMed:20805881, PubMed:22844097).
Also catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes (PubMed:16876125, PubMed:19060136, PubMed:22457352).
Gyrase from M.tuberculosis has higher decatenation than supercoiling activity compared to E.coli; as M.tuberculosis only has 1 type II topoisomerase, gyrase has to fulfill the decatenation function of topoisomerase IV as well (PubMed:16876125, PubMed:22457352, PubMed:23869946).
At comparable concentrations M.tuberculosis gyrase cannot introduce as many negative supercoils into DNA as the E.coli enzyme, and its ATPase activity is lower, perhaps because it does not couple DNA wrapping and ATP binding as well as E.coli (PubMed:22457352).
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:15047530).
In the presence of quinolones this intermediate can be trapped and is used as an indicator of drug toxicity (PubMed:16377674, PubMed:23869946).
DNA gyrase is intrinsically more resistant to fluoroquinolone drugs than in E.coli, mutating it to resemble E.coli increases its susceptibility to fluoroquinolones (most quinolone-resistant mutations are in this subunit) (PubMed:18426901).
Gyrase from M.tuberculosis is usually assayed in the presence of potassium glutamate (KGlu); KGlu stimulates supercoiling but inhibits DNA relaxation activity, and has concentration-dependent effects on GyrA-box mutants (PubMed:16876125, PubMed:23869946).

Catalytic activity

  • ATP-dependent breakage, passage and rejoining of double-stranded DNA.
    EC:5.6.2.2 (UniProtKB | ENZYME | Rhea)

Cofactor

Ca2+ (UniProtKB | Rhea| CHEBI:29108 )

Note: May bind up to 2 Ca2+ per subunit, Ca2+ does not substitute for supercoiling activity, but is required for relaxation, probably by an interaction with this subunit (PubMed:22844097).
This subunit has altered protease sensitivity in the presence of Ca2+, which might reflect regulation (PubMed:22844097).

Activity regulation

DNA supercoiling inhibited by (fluoro)quinoline antibiotics such as sparfloxacin and levofloxacin, which usually act on GyrA (PubMed:15047530, PubMed:17015625).
DNA supercoiling inhibited by the coumarin antibiotic novobiocin which acts on GyrB (PubMed:16876125).
Quinolones lead to gyrase-mediated dsDNA cleavage while preventing reclosure (PubMed:15047530, PubMed:16876125, PubMed:23869946).
DNA supercoiling activity inhibited by aminopyrazinamide and pyrrolamide derivatives, probably via effects on the GyrB subunit (PubMed:23268609, PubMed:24126580).
DNA relaxation inhibited by ATP and its analogs (PubMed:16876125).
DNA supercoiling, relaxation, decatenation and quinolone-promoted DNA cleavage are inhibited by MfpA (50% inhibition occurs at 2 uM), inhibition of gyrase activities is enhanced in a concentration-dependent manner by MfpA (PubMed:19060136).

Features

Showing features for active site, binding site.

TypeIDPosition(s)Description
Active site129O-(5'-phospho-DNA)-tyrosine intermediate
Binding site504Ca2+ (UniProtKB | ChEBI)
Binding site506Ca2+ (UniProtKB | ChEBI)
Binding site508Ca2+ (UniProtKB | ChEBI)
Binding site515Ca2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentchromosome
Cellular Componentcytoplasm
Cellular ComponentDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
Cellular Componentpeptidoglycan-based cell wall
Cellular Componentplasma membrane
Molecular FunctionATP binding
Molecular FunctionATP hydrolysis activity
Molecular FunctionDNA binding
Molecular FunctionDNA negative supercoiling activity
Molecular FunctionDNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
Molecular Functionmagnesium ion binding
Biological ProcessDNA topological change
Biological ProcessDNA-templated DNA replication
Biological Processresponse to antibiotic

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    DNA gyrase subunit A
  • EC number
  • Alternative names
    • Type IIA topoisomerase subunit GyrA

Gene names

    • Name
      gyrA
    • ORF names
      MTCY10H4.04
    • Ordered locus names
      Rv0006

Organism names

Accessions

  • Primary accession
    P9WG47
  • Secondary accessions
    • J9VB15
    • P71574
    • P97136
    • Q07702

Proteomes

Organism-specific databases

Phenotypes & Variants

Features

Showing features for mutagenesis, natural variant.

TypeIDPosition(s)Description
Mutagenesis80Slight resistance to fluoroquinolones. Hypersusceptibile, 2- to 14-fold higher sensitivity to fluoroquinolones, 2- to 8-fold more efficient in fluoroquinolone-induced DNA cleavage; when associated with G-90.
Mutagenesis88Confers fluoroquinolone resistance, IC50 is 2- to 26-fold higher than wild-type.
Mutagenesis88Confers fluoroquinolone resistance, IC50 is 3- to 43-fold higher than wild-type, in strains H37Ra and H37Rv.
Natural variant90confers ciprofloxacin resistance, in clinical isolate
Mutagenesis904- to 16-fold more efficient in fluoroquinolone-induced DNA cleavage alone. Hypersusceptibile, 2- to 14-fold higher sensitivity to fluoroquinolones, 2- to 8-fold more efficient in fluoroquinolone-induced DNA cleavage; when associated with A-80.
Mutagenesis90Increased susceptibility to fluoroquinolones (makes sequence more like E.coli), supercoiling, relaxation, decatenation activities still inhibited by MfpA.
Mutagenesis9017-fold increased resistance to fluoroquinolones, 4- to 8-fold reduction in fluoroquinolone-induced DNA cleavage.
Mutagenesis90-9480-fold increased resistance to fluoroquinolones, 32- to 64-fold reduction in fluoroquinolone-induced DNA cleavage.
Natural variant91confers ciprofloxacin resistance, in clinical isolate
Natural variant94confers ciprofloxacin resistance, in clinical isolate
Natural variant94confers ciprofloxacin resistance, in clinical isolate
Natural variant94confers ciprofloxacin resistance, in clinical isolate
Natural variant94confers ciprofloxacin resistance, in clinical isolate
Natural variant94confers ciprofloxacin resistance, in clinical isolate
Mutagenesis9425- 45-fold increased resistance to fluoroquinolones, 4- to 8-fold reduction in fluoroquinolone-induced DNA cleavage. Supercoiling, relaxation, decatenation activities no longer inhibited by MfpA.
Mutagenesis94Confers ofloxacin resistance.
Mutagenesis504-514Significant reduction in DNA wrapping and supercoiling activity, no change in decatanation or relaxation activities.
Mutagenesis508-509Slight reduction in supercoiling activity.
Mutagenesis538Wild-type decatenase activity (changes residue to match E.coli).
Mutagenesis540No change in supercoiling activity, wild-type decatenation or fluoroquinolone-induced DNA cleavage.
Mutagenesis540-543No supercoiling activity, almost wild-type decatenation activity, wild-type fluoroquinolone-induced DNA cleavage.
Mutagenesis541Reduced supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage.
Mutagenesis543Reduced supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage.
Mutagenesis543No supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage.
Mutagenesis544-545Wild-type decatenase activity (changes residues to match E.coli).
Mutagenesis746Wild-type supercoiling, decatenation and fluoroquinolone-induced DNA cleavage.
Mutagenesis746-749No supercoiling or decatenation activity, decreased fluoroquinolone-induced DNA cleavage.
Mutagenesis747Wild-type supercoiling, decatenation and fluoroquinolone-induced DNA cleavage.
Mutagenesis749No supercoiling or decatenation activity, decreased fluoroquinolone-induced DNA cleavage.

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 7 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

Chemistry

PTM/Processing

Features

Showing features for initiator methionine, modified residue, chain.

TypeIDPosition(s)Description
Initiator methionine1Removed
Modified residue2N-acetylthreonine
ChainPRO_00001452432-838DNA gyrase subunit A

Keywords

Proteomic databases

PTM databases

Interaction

Subunit

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 (PubMed:15047530).

Protein-protein interaction databases

Chemistry

Family & Domains

Features

Showing features for domain, region, motif.

TypeIDPosition(s)Description
Domain41-510Topo IIA-type catalytic
Domain504-516EF-hand
Region514-838C-terminal domain CTD
Motif537-543GyrA-box
Motif743-749GyrA-box-1

Domain

The N-terminal domain (residues 1-502, also called GA57BK) forms a dimer; when reconstituted with intact GyrB or the C-terminus of GyrB (residues 448-675) can catalyze quinolone-mediated DNA breaks (PubMed:20805881).
The C-terminal domain (CTD, residues 514-838) contains 6 tandemly repeated subdomains known as blades, each of which is composed of a 4-stranded antiparallel beta-sheet (PubMed:22457352, PubMed:23869946).
The blades form a circular-shaped beta-pinwheel fold arranged in a spiral around a screw axis, which binds DNA (PubMed:22457352, PubMed:23869946).
Unlike in E.coli, isolated CTD both binds and wraps DNA and is able to introduce writhe into DNA, but the holoenzyme in M.tuberculosis is missing the GyrA acidic tail found in E.coli and thus does not couple DNA wrapping and ATP binding as well as E.coli (PubMed:22457352).
There are 2 GyrA-boxes in the CTD; mutations in GyrA-box (residues 537-543, the canonical box) affect supercoiling but not decatenation, those in GyrA-box-1 (residues 743-749, conserved in some Actinobacteria) affect both, suggesting there is a novel DNA-binding pathway in M.tuberculosis compared to E.coli (PubMed:23869946).

Sequence similarities

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

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    838
  • Mass (Da)
    92,274
  • Last updated
    2014-04-16 v1
  • Checksum
    84DAFE13D74D76D7
MTDTTLPPDDSLDRIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN

Features

Showing features for sequence conflict.

TypeIDPosition(s)Description
Sequence conflict83in Ref. 4; AAC36878
Sequence conflict712in Ref. 1; AAA83017

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
L27512
EMBL· GenBank· DDBJ
AAA83017.1
EMBL· GenBank· DDBJ
Genomic DNA
JX303241
EMBL· GenBank· DDBJ
AFR90330.1
EMBL· GenBank· DDBJ
Genomic DNA
AL123456
EMBL· GenBank· DDBJ
CCP42728.1
EMBL· GenBank· DDBJ
Genomic DNA
L11919
EMBL· GenBank· DDBJ
AAC36878.1
EMBL· GenBank· DDBJ
Unassigned DNA
X72872
EMBL· GenBank· DDBJ
CAA51386.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. Our staff consists of biologists and biochemists that are not trained to give medical advice.
We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.
FeedbackHelp