P9WG47 · GYRA_MYCTU
- ProteinDNA gyrase subunit A
- GenegyrA
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids838 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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).
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
Cofactor
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).
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).
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.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromosome | |
Cellular Component | cytoplasm | |
Cellular Component | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex | |
Cellular Component | peptidoglycan-based cell wall | |
Cellular Component | plasma membrane | |
Molecular Function | ATP binding | |
Molecular Function | ATP hydrolysis activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA negative supercoiling activity | |
Molecular Function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity | |
Molecular Function | magnesium ion binding | |
Biological Process | DNA topological change | |
Biological Process | DNA-templated DNA replication | |
Biological Process | response to antibiotic |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA gyrase subunit A
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageBacteria > Actinomycetota > Actinomycetes > Mycobacteriales > Mycobacteriaceae > Mycobacterium > Mycobacterium tuberculosis complex
Accessions
- Primary accessionP9WG47
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Phenotypes & Variants
Features
Showing features for mutagenesis, natural variant.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 80 | Slight 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. | ||||
Sequence: T → A | ||||||
Mutagenesis | 88 | Confers fluoroquinolone resistance, IC50 is 2- to 26-fold higher than wild-type. | ||||
Sequence: G → A | ||||||
Mutagenesis | 88 | Confers fluoroquinolone resistance, IC50 is 3- to 43-fold higher than wild-type, in strains H37Ra and H37Rv. | ||||
Sequence: G → C | ||||||
Natural variant | 90 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: A → V | ||||||
Mutagenesis | 90 | 4- 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. | ||||
Sequence: A → G | ||||||
Mutagenesis | 90 | Increased susceptibility to fluoroquinolones (makes sequence more like E.coli), supercoiling, relaxation, decatenation activities still inhibited by MfpA. | ||||
Sequence: A → S | ||||||
Mutagenesis | 90 | 17-fold increased resistance to fluoroquinolones, 4- to 8-fold reduction in fluoroquinolone-induced DNA cleavage. | ||||
Sequence: A → V | ||||||
Mutagenesis | 90-94 | 80-fold increased resistance to fluoroquinolones, 32- to 64-fold reduction in fluoroquinolone-induced DNA cleavage. | ||||
Sequence: ASIYD → VSIYG | ||||||
Natural variant | 91 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: S → P | ||||||
Natural variant | 94 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: D → A | ||||||
Natural variant | 94 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: D → G | ||||||
Natural variant | 94 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: D → H | ||||||
Natural variant | 94 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: D → N | ||||||
Natural variant | 94 | confers ciprofloxacin resistance, in clinical isolate | ||||
Sequence: D → Y | ||||||
Mutagenesis | 94 | 25- 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. | ||||
Sequence: D → G or H | ||||||
Mutagenesis | 94 | Confers ofloxacin resistance. | ||||
Sequence: D → H | ||||||
Mutagenesis | 504-514 | Significant reduction in DNA wrapping and supercoiling activity, no change in decatanation or relaxation activities. | ||||
Sequence: DVSDEDLIARE → AVSDAALIARA | ||||||
Mutagenesis | 508-509 | Slight reduction in supercoiling activity. | ||||
Sequence: ED → AA | ||||||
Mutagenesis | 538 | Wild-type decatenase activity (changes residue to match E.coli). | ||||
Sequence: K → R | ||||||
Mutagenesis | 540 | No change in supercoiling activity, wild-type decatenation or fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A | ||||||
Mutagenesis | 540-543 | No supercoiling activity, almost wild-type decatenation activity, wild-type fluoroquinolone-induced DNA cleavage. | ||||
Sequence: GGKG → AAKA | ||||||
Mutagenesis | 541 | Reduced supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A | ||||||
Mutagenesis | 543 | Reduced supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A | ||||||
Mutagenesis | 543 | No supercoiling activity, wild-type decatenation and fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → K | ||||||
Mutagenesis | 544-545 | Wild-type decatenase activity (changes residues to match E.coli). | ||||
Sequence: VQ → KS | ||||||
Mutagenesis | 746 | Wild-type supercoiling, decatenation and fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A | ||||||
Mutagenesis | 746-749 | No supercoiling or decatenation activity, decreased fluoroquinolone-induced DNA cleavage. | ||||
Sequence: GGKG → AAKA | ||||||
Mutagenesis | 747 | Wild-type supercoiling, decatenation and fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A | ||||||
Mutagenesis | 749 | No supercoiling or decatenation activity, decreased fluoroquinolone-induced DNA cleavage. | ||||
Sequence: G → A |
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.
Chemistry
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Initiator methionine | 1 | Removed | ||||
Sequence: M | ||||||
Modified residue | 2 | N-acetylthreonine | ||||
Sequence: T | ||||||
Chain | PRO_0000145243 | 2-838 | DNA gyrase subunit A | |||
Sequence: TDTTLPPDDSLDRIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN |
Keywords
- PTM
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
Structure
Family & Domains
Features
Showing features for domain, region, motif.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 41-510 | Topo IIA-type catalytic | ||||
Sequence: LPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIAADGDVSDEDL | ||||||
Domain | 504-516 | EF-hand | ||||
Sequence: DVSDEDLIAREDV | ||||||
Region | 514-838 | C-terminal domain CTD | ||||
Sequence: EDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGVQGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN | ||||||
Motif | 537-543 | GyrA-box | ||||
Sequence: QKRGGKG | ||||||
Motif | 743-749 | GyrA-box-1 | ||||
Sequence: QGRGGKG |
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).
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 statusComplete
- Length838
- Mass (Da)92,274
- Last updated2014-04-16 v1
- Checksum84DAFE13D74D76D7
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 83 | in Ref. 4; AAC36878 | ||||
Sequence: N → K | ||||||
Sequence conflict | 712 | in Ref. 1; AAA83017 | ||||
Sequence: L → V |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |