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DNA gyrase subunit A (EC 5.99.1.3)

 GYRA_ECOLI              Reviewed;         875 AA.
P0AES4; P09097;
20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
20-DEC-2005, sequence version 1.
18-JUL-2018, entry version 127.
RecName: Full=DNA gyrase subunit A {ECO:0000255|HAMAP-Rule:MF_01897};
EC=5.99.1.3 {ECO:0000255|HAMAP-Rule:MF_01897, ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:9278055};
Name=gyrA {ECO:0000255|HAMAP-Rule:MF_01897};
Synonyms=hisW, nalA {ECO:0000303|PubMed:337300}, parD;
OrderedLocusNames=b2231, JW2225;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2828631; DOI=10.1016/0022-2836(87)90479-7;
Swanberg S.L., Wang J.C.;
"Cloning and sequencing of the Escherichia coli gyrA gene coding for
the A subunit of DNA gyrase.";
J. Mol. Biol. 197:729-736(1987).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12 / KL16;
PubMed=2830458; DOI=10.1007/BF00338386;
Yoshida H., Kojima T., Yamagishi J., Nakamura S.;
"Quinolone-resistant mutations of the gyrA gene of Escherichia coli.";
Mol. Gen. Genet. 211:1-7(1988).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS QUINOLONE-RESISTANTS
ASN-87 AND ILE-MET-MET-ILE-798.
STRAIN=OV6;
PubMed=2834621; DOI=10.1111/j.1365-2958.1987.tb01932.x;
Hussain K., Elliott E.J., Salmond G.P.C.;
"The parD- mutant of Escherichia coli also carries a gyrAam mutation.
The complete sequence of gyrA.";
Mol. Microbiol. 1:259-273(1987).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS QUINOLONE-RESISTANT
GLU-678 AND SER-828.
STRAIN=227;
PubMed=2548439; DOI=10.1128/AAC.33.6.886;
Cullen M.E., Wyke A.W., Kuroda R., Fisher L.M.;
"Cloning and characterization of a DNA gyrase A gene from Escherichia
coli that confers clinical resistance to 4-quinolones.";
Antimicrob. Agents Chemother. 33:886-894(1989).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=9205837; DOI=10.1093/dnares/4.2.91;
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.;
"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.";
DNA Res. 4:91-113(1997).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[8]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-88, AND PARTIAL PROTEIN
SEQUENCE.
PubMed=3029031; DOI=10.1128/jb.169.3.1272-1278.1987;
Menzel R., Gellert M.;
"Fusions of the Escherichia coli gyrA and gyrB control regions to the
galactokinase gene are inducible by coumermycin treatment.";
J. Bacteriol. 169:1272-1278(1987).
[9]
PROTEIN SEQUENCE OF 17-24; 61-66 AND 123-126, FUNCTION, ACTIVE SITE,
REACTION MECHANISM, AND DNA-BINDING.
PubMed=3031051;
Horowitz D.S., Wang J.C.;
"Mapping the active site tyrosine of Escherichia coli DNA gyrase.";
J. Biol. Chem. 262:5339-5344(1987).
[10]
FUNCTION IN GENERATING NEGATIVELY SUPERCOILED DNA, CATALYTIC ACTIVITY,
AND ATP-DEPENDENCE.
PubMed=186775; DOI=10.1073/pnas.73.11.3872;
Gellert M., Mizuuchi K., O'Dea M.H., Nash H.A.;
"DNA gyrase: an enzyme that introduces superhelical turns into DNA.";
Proc. Natl. Acad. Sci. U.S.A. 73:3872-3876(1976).
[11]
FUNCTION IN RELAXING SUPERCOILED DNA, AND ENZYME REGULATION.
PubMed=337300; DOI=10.1073/pnas.74.11.4772;
Gellert M., Mizuuchi K., O'Dea M.H., Itoh T., Tomizawa J.I.;
"Nalidixic acid resistance: a second genetic character involved in DNA
gyrase activity.";
Proc. Natl. Acad. Sci. U.S.A. 74:4772-4776(1977).
[12]
VARIANTS QUINOLONE-RESISTANT SER-67; CYS-81; LEU-83; TRP-83; PRO-84;
ASN-87 AND HIS-106.
STRAIN=K12 / KL16;
PubMed=2168148; DOI=10.1128/AAC.34.6.1271;
Yoshida H., Bogaki M., Nakamura M., Nakamura S.;
"Quinolone resistance-determining region in the DNA gyrase gyrA gene
of Escherichia coli.";
Antimicrob. Agents Chemother. 34:1271-1272(1990).
[13]
VARIANTS QUINOLONE-RESISTANT LEU-83; TRP-83 AND VAL-87.
PubMed=1850972; DOI=10.1128/AAC.35.2.387;
Oram M., Fisher L.M.;
"4-quinolone resistance mutations in the DNA gyrase of Escherichia
coli clinical isolates identified by using the polymerase chain
reaction.";
Antimicrob. Agents Chemother. 35:387-389(1991).
[14]
MUTAGENESIS OF SER-83 AND GLN-106.
STRAIN=K12;
PubMed=1850970; DOI=10.1128/AAC.35.2.335;
Hallett P., Maxwell A.;
"Novel quinolone resistance mutations of the Escherichia coli DNA
gyrase A protein: enzymatic analysis of the mutant proteins.";
Antimicrob. Agents Chemother. 35:335-340(1991).
[15]
INHIBITION BY TOXIN PROTEIN CCDB, AND MUTAGENESIS OF ARG-462.
STRAIN=K12;
PubMed=1324324; DOI=10.1016/0022-2836(92)90629-X;
Bernard P., Couturier M.;
"Cell killing by the F plasmid CcdB protein involves poisoning of DNA-
topoisomerase II complexes.";
J. Mol. Biol. 226:735-745(1992).
[16]
MUTAGENESIS OF ARG-462.
PubMed=8254658; DOI=10.1006/jmbi.1993.1609;
Bernard P., Kezdy K.E., Van Melderen L., Steyaert J., Wyns L.,
Pato M.L., Higgins P.N., Couturier M.;
"The F plasmid CcdB protein induces efficient ATP-dependent DNA
cleavage by gyrase.";
J. Mol. Biol. 234:534-541(1993).
[17]
FUNCTION, AND ENZYME REGULATION.
PubMed=7811004; DOI=10.1128/AAC.38.9.1966;
Nakada N., Gmuender H., Hirata T., Arisawa M.;
"Mechanism of inhibition of DNA gyrase by cyclothialidine, a novel DNA
gyrase inhibitor.";
Antimicrob. Agents Chemother. 38:1966-1973(1994).
[18]
INHIBITION BY TOXIN PROTEIN CCDB, REJUVENATION BY CCDA, AND SUBUNIT.
PubMed=8604132; DOI=10.1006/jmbi.1996.0102;
Maki S., Takiguchi S., Horiuchi T., Sekimizu K., Miki T.;
"Partner switching mechanisms in inactivation and rejuvenation of
Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA
(CcdA).";
J. Mol. Biol. 256:473-482(1996).
[19]
FUNCTION, AND DOMAIN.
PubMed=8962066; DOI=10.1073/pnas.93.25.14416;
Kampranis S.C., Maxwell A.;
"Conversion of DNA gyrase into a conventional type II topoisomerase.";
Proc. Natl. Acad. Sci. U.S.A. 93:14416-14421(1996).
[20]
FUNCTION, ENZYME REGULATION, SUBUNIT, AND DNA-BINDING.
STRAIN=K12 / N2879;
PubMed=9148951; DOI=10.1074/jbc.272.20.13302;
Funatsuki K., Tanaka R., Inagaki S., Konno H., Katoh K., Nakamura H.;
"acrB mutation located at carboxyl-terminal region of gyrase B subunit
reduces DNA binding of DNA gyrase.";
J. Biol. Chem. 272:13302-13308(1997).
[21]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[22]
FUNCTION.
PubMed=9334322; DOI=10.1101/gad.11.19.2580;
Zechiedrich E.L., Khodursky A.B., Cozzarelli N.R.;
"Topoisomerase IV, not gyrase, decatenates products of site-specific
recombination in Escherichia coli.";
Genes Dev. 11:2580-2592(1997).
[23]
IDENTIFICATION AND DISCUSSION OF GYRA-BOX, AND DOMAIN.
PubMed=9426128; DOI=10.1046/j.1365-2958.1997.6242005.x;
Ward D.V., Newton A.;
"Requirement of topoisomerase IV parC and parE genes for cell cycle
progression and developmental regulation in Caulobacter crescentus.";
Mol. Microbiol. 26:897-910(1997).
[24]
FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND MUTAGENESIS OF ARG-32;
ARG-47; HIS-78 AND HIS-80.
PubMed=12051842; DOI=10.1016/S0022-2836(02)00048-7;
Hockings S.C., Maxwell A.;
"Identification of four GyrA residues involved in the DNA breakage-
reunion reaction of DNA gyrase.";
J. Mol. Biol. 318:351-359(2002).
[25]
FUNCTION, AND MUTAGENESIS OF 560-GLN--GLY-566.
PubMed=16332690; DOI=10.1074/jbc.M511160200;
Kramlinger V.M., Hiasa H.;
"The 'GyrA-box' is required for the ability of DNA gyrase to wrap DNA
and catalyze the supercoiling reaction.";
J. Biol. Chem. 281:3738-3742(2006).
[26]
FUNCTION.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=17400739; DOI=10.1128/JB.00083-07;
Champion K., Higgins N.P.;
"Growth rate toxicity phenotypes and homeostatic supercoil control
differentiate Escherichia coli from Salmonella enterica serovar
Typhimurium.";
J. Bacteriol. 189:5839-5849(2007).
[27]
FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
PubMed=18642932; DOI=10.1021/bi800480j;
Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A.,
Palumbo M.;
"DNA gyrase requires DNA for effective two-site coordination of
divalent metal ions: further insight into the mechanism of enzyme
action.";
Biochemistry 47:8538-8545(2008).
[28]
FUNCTION, AND ENZYME REGULATION.
PubMed=19060136; DOI=10.1128/JB.01205-08;
Merens A., Matrat S., Aubry A., Lascols C., Jarlier V., Soussy C.J.,
Cavallo J.D., Cambau E.;
"The pentapeptide repeat proteins MfpAMt and QnrB4 exhibit opposite
effects on DNA gyrase catalytic reactions and on the ternary gyrase-
DNA-quinolone complex.";
J. Bacteriol. 191:1587-1594(2009).
[29]
FUNCTION, AND ENZYME REGULATION.
PubMed=20356737; DOI=10.1016/j.bmcl.2010.03.052;
Ronkin S.M., Badia M., Bellon S., Grillot A.L., Gross C.H.,
Grossman T.H., Mani N., Parsons J.D., Stamos D., Trudeau M., Wei Y.,
Charifson P.S.;
"Discovery of pyrazolthiazoles as novel and potent inhibitors of
bacterial gyrase.";
Bioorg. Med. Chem. Lett. 20:2828-2831(2010).
[30]
FUNCTION, DOMAIN, DNA-BINDING, AND MUTAGENESIS OF 842-PRO--ALA-856 AND
854-SER--GLU-875.
PubMed=22457353; DOI=10.1074/jbc.M112.345678;
Tretter E.M., Berger J.M.;
"Mechanisms for defining supercoiling set point of DNA gyrase
orthologs: I. A nonconserved acidic C-terminal tail modulates
Escherichia coli gyrase activity.";
J. Biol. Chem. 287:18636-18644(2012).
[31]
FUNCTION, DNA-BINDING, AND MUTAGENESIS OF 842-PRO--ALA-856.
PubMed=22457352; DOI=10.1074/jbc.M112.345736;
Tretter E.M., Berger J.M.;
"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.";
J. Biol. Chem. 287:18645-18654(2012).
[32]
FUNCTION, AND ENZYME REGULATION.
PubMed=23294697; DOI=10.1016/j.bmcl.2012.11.073;
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.;
"Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase
IV (ParE), Part II: development of inhibitors with broad spectrum,
Gram-negative antibacterial activity.";
Bioorg. Med. Chem. Lett. 23:1537-1543(2013).
[33]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522, AND CATALYTIC
ACTIVITY.
PubMed=9278055; DOI=10.1038/42294;
Morais Cabral J.H., Jackson A.P., Smith C.V., Shikotra N., Maxwell A.,
Liddington R.C.;
"Crystal structure of the breakage-reunion domain of DNA gyrase.";
Nature 388:903-906(1997).
[34]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 363-494 IN COMPLEX WITH CCBD,
AND SUBUNIT.
PubMed=15854646; DOI=10.1016/j.jmb.2005.03.049;
Dao-Thi M.H., Van Melderen L., De Genst E., Afif H., Buts L., Wyns L.,
Loris R.;
"Molecular basis of gyrase poisoning by the addiction toxin CcdB.";
J. Mol. Biol. 348:1091-1102(2005).
[35]
X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 535-841, AND DOMAIN.
STRAIN=K12;
PubMed=15897198; DOI=10.1074/jbc.M502838200;
Ruthenburg A.J., Graybosch D.M., Huetsch J.C., Verdine G.L.;
"A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal
domain imparts unidirectional supercoiling bias.";
J. Biol. Chem. 280:26177-26184(2005).
[36]
X-RAY CRYSTALLOGRAPHY (2.62 ANGSTROMS) OF 1-525 IN COMPLEX WITH
ANTIBIOTIC, FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
PubMed=19965760; DOI=10.1126/science.1179123;
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.;
"A crystal structure of the bifunctional antibiotic simocyclinone D8,
bound to DNA gyrase.";
Science 326:1415-1418(2009).
-!- 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
(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).
{ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:16332690,
ECO:0000269|PubMed:17400739, ECO:0000269|PubMed:18642932,
ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19060136,
ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:20356737,
ECO:0000269|PubMed:22457352, ECO:0000269|PubMed:22457353,
ECO:0000269|PubMed:23294697, ECO:0000269|PubMed:3031051,
ECO:0000269|PubMed:337300, ECO:0000269|PubMed:7811004,
ECO:0000269|PubMed:8962066, ECO:0000269|PubMed:9148951,
ECO:0000269|PubMed:9334322}.
-!- FUNCTION: 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 ACTIVITY: ATP-dependent breakage, passage and rejoining
of double-stranded DNA. {ECO:0000255|HAMAP-Rule:MF_01897,
ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:18642932,
ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19965760,
ECO:0000269|PubMed:9278055}.
-!- ENZYME REGULATION: 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).
{ECO:0000269|PubMed:19060136, ECO:0000269|PubMed:20356737,
ECO:0000269|PubMed:23294697, ECO:0000269|PubMed:337300,
ECO:0000269|PubMed:7811004, ECO:0000269|PubMed:9148951}.
-!- SUBUNIT: 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
GyrA(2)CcdB(2) is effected by CcdA (PubMed:15854646,
PubMed:1324324, PubMed:8254658, PubMed:8604132).
{ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:1324324,
ECO:0000269|PubMed:15854646, ECO:0000269|PubMed:18642932,
ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:8254658,
ECO:0000269|PubMed:8604132, ECO:0000269|PubMed:9148951}.
-!- INTERACTION:
Self; NbExp=5; IntAct=EBI-547129, EBI-547129;
P0AES6:gyrB; NbExp=7; IntAct=EBI-547129, EBI-541911;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01897}.
-!- DOMAIN: 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).
{ECO:0000269|PubMed:8962066}.
-!- DOMAIN: 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).
{ECO:0000269|PubMed:15897198, ECO:0000269|PubMed:16332690,
ECO:0000269|PubMed:22457353, ECO:0000305|PubMed:9426128}.
-!- 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). {ECO:0000269|PubMed:1324324,
ECO:0000269|PubMed:3031051, ECO:0000269|PubMed:8254658,
ECO:0000305|PubMed:12051842}.
-!- MISCELLANEOUS: 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. {ECO:0000255|HAMAP-Rule:MF_01897,
ECO:0000269|PubMed:17400739, ECO:0000269|PubMed:22457352}.
-!- SIMILARITY: Belongs to the type II topoisomerase GyrA/ParC subunit
family. {ECO:0000255|HAMAP-Rule:MF_01897}.
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EMBL; X06373; CAA29676.1; -; Genomic_DNA.
EMBL; X06744; CAA29919.1; -; Genomic_DNA.
EMBL; M15631; AAA23948.1; -; Genomic_DNA.
EMBL; U00096; AAC75291.1; -; Genomic_DNA.
EMBL; AP009048; BAA16048.1; -; Genomic_DNA.
EMBL; Y00544; CAA68611.1; -; Genomic_DNA.
PIR; S02340; ITECAP.
RefSeq; NP_416734.1; NC_000913.3.
RefSeq; WP_001281242.1; NZ_LN832404.1.
PDB; 1AB4; X-ray; 2.80 A; A=30-522.
PDB; 1X75; X-ray; 2.80 A; A/B=363-494.
PDB; 1ZI0; X-ray; 2.60 A; A/B=535-841.
PDB; 2Y3P; X-ray; 2.62 A; A/B=2-523.
PDB; 3NUH; X-ray; 3.10 A; A=1-525.
PDB; 4ELY; X-ray; 1.93 A; A/B=363-497.
PDBsum; 1AB4; -.
PDBsum; 1X75; -.
PDBsum; 1ZI0; -.
PDBsum; 2Y3P; -.
PDBsum; 3NUH; -.
PDBsum; 4ELY; -.
ProteinModelPortal; P0AES4; -.
SMR; P0AES4; -.
BioGrid; 4262132; 294.
ComplexPortal; CPX-2177; GyrA-GyrB complex.
DIP; DIP-36179N; -.
IntAct; P0AES4; 54.
MINT; P0AES4; -.
STRING; 316385.ECDH10B_2390; -.
BindingDB; P0AES4; -.
ChEMBL; CHEMBL1858; -.
DrugBank; DB00537; Ciprofloxacin.
SWISS-2DPAGE; P0AES4; -.
EPD; P0AES4; -.
PaxDb; P0AES4; -.
PRIDE; P0AES4; -.
EnsemblBacteria; AAC75291; AAC75291; b2231.
EnsemblBacteria; BAA16048; BAA16048; BAA16048.
GeneID; 946614; -.
KEGG; ecj:JW2225; -.
KEGG; eco:b2231; -.
PATRIC; fig|1411691.4.peg.4; -.
EchoBASE; EB0418; -.
EcoGene; EG10423; gyrA.
eggNOG; ENOG4105C24; Bacteria.
eggNOG; COG0188; LUCA.
HOGENOM; HOG000076278; -.
InParanoid; P0AES4; -.
KO; K02469; -.
OMA; THHWLLF; -.
PhylomeDB; P0AES4; -.
BioCyc; EcoCyc:EG10423-MONOMER; -.
BioCyc; MetaCyc:EG10423-MONOMER; -.
EvolutionaryTrace; P0AES4; -.
PRO; PR:P0AES4; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005694; C:chromosome; IEA:InterPro.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0016020; C:membrane; HDA:UniProtKB.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
GO; GO:0034335; F:DNA supercoiling activity; IDA:UniProtKB.
GO; GO:0003918; F:DNA topoisomerase type II (ATP-hydrolyzing) activity; IDA:CACAO.
GO; GO:0008094; F:DNA-dependent ATPase activity; IDA:EcoliWiki.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0006265; P:DNA topological change; IMP:EcoliWiki.
GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
GO; GO:0042493; P:response to drug; IMP:EcoliWiki.
GO; GO:0006351; P:transcription, DNA-templated; IDA:EcoliWiki.
Gene3D; 1.10.268.10; -; 1.
Gene3D; 2.120.10.90; -; 1.
Gene3D; 3.90.199.10; -; 3.
HAMAP; MF_01897; GyrA; 1.
InterPro; IPR005743; GyrA.
InterPro; IPR006691; GyrA/parC_rep.
InterPro; IPR035516; Gyrase/topoIV_suA_C.
InterPro; IPR013760; Topo_IIA-like_dom_sf.
InterPro; IPR002205; Topo_IIA_A/C.
InterPro; IPR013758; Topo_IIA_A/C_ab.
InterPro; IPR013757; Topo_IIA_A_a_sf.
Pfam; PF03989; DNA_gyraseA_C; 6.
Pfam; PF00521; DNA_topoisoIV; 1.
SMART; SM00434; TOP4c; 1.
SUPFAM; SSF101904; SSF101904; 1.
SUPFAM; SSF56719; SSF56719; 1.
1: Evidence at protein level;
3D-structure; Antibiotic resistance; ATP-binding; Complete proteome;
Cytoplasm; Direct protein sequencing; DNA-binding; Isomerase;
Nucleotide-binding; Reference proteome; Topoisomerase.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:3029031}.
CHAIN 2 875 DNA gyrase subunit A.
/FTId=PRO_0000145232.
REGION 531 841 C-terminal domain (CTD).
{ECO:0000303|PubMed:15897198}.
REGION 842 875 Acidic tail.
{ECO:0000303|PubMed:22457353}.
MOTIF 560 566 GyrA-box. {ECO:0000255|HAMAP-
Rule:MF_01897,
ECO:0000303|PubMed:9426128}.
ACT_SITE 122 122 O-(5'-phospho-DNA)-tyrosine intermediate.
{ECO:0000255|HAMAP-Rule:MF_01897,
ECO:0000269|PubMed:3031051}.
VARIANT 67 67 A -> S (in PPA-10; quinolone-resistant).
{ECO:0000269|PubMed:2168148}.
VARIANT 81 81 G -> C (in NAL-97; quinolone-resistant).
{ECO:0000269|PubMed:2168148}.
VARIANT 83 83 S -> L (in NAL-51, NAL-112, NAL-118, NAL-
119 and strains 58, 158, 218, 231 and
235; quinolone-resistant).
{ECO:0000269|PubMed:1850972,
ECO:0000269|PubMed:2168148}.
VARIANT 83 83 S -> W (in PPA-18 and strains 233 and
227; quinolone-resistant).
{ECO:0000269|PubMed:1850972,
ECO:0000269|PubMed:2168148,
ECO:0000269|PubMed:2548439}.
VARIANT 84 84 A -> P (in PPA-05; quinolone-resistant).
{ECO:0000269|PubMed:2168148}.
VARIANT 87 87 D -> N (in NAL-113 and OV6; quinolone-
resistant). {ECO:0000269|PubMed:2168148,
ECO:0000269|PubMed:2834621}.
VARIANT 87 87 D -> V (in strain: 202; partially
quinolone-resistant).
{ECO:0000269|PubMed:1850972}.
VARIANT 106 106 Q -> H (in NAL-89; quinolone-resistant).
{ECO:0000269|PubMed:2168148}.
VARIANT 678 678 D -> E (in strain: 227).
{ECO:0000269|PubMed:2548439}.
VARIANT 798 798 I -> IMMI (in strain OV6; quinolone-
resistant). {ECO:0000269|PubMed:2834621}.
VARIANT 828 828 A -> S (in strain: 227).
{ECO:0000269|PubMed:2548439}.
MUTAGEN 32 32 R->A,Q: Nearly abolishes DNA
supercoiling. Reduces quinolone-induced
DNA cleavage and relaxation.
{ECO:0000269|PubMed:12051842}.
MUTAGEN 47 47 R->Q: Nearly abolishes DNA supercoiling.
Reduces quinolone-induced DNA cleavage.
Slightly reduces DNA relaxation.
{ECO:0000269|PubMed:12051842}.
MUTAGEN 78 78 H->A: Nearly abolishes DNA supercoiling.
Reduces quinolone-induced DNA cleavage
and DNA relaxation.
{ECO:0000269|PubMed:12051842}.
MUTAGEN 80 80 H->A: Reduces DNA supercoiling. Slightly
reduces quinolone-induced DNA cleavage.
No effect on DNA relaxation.
{ECO:0000269|PubMed:12051842}.
MUTAGEN 83 83 S->A: Resistant to fluoroquinolones.
{ECO:0000269|PubMed:1850970}.
MUTAGEN 106 106 Q->R: Resistant to fluoroquinolones.
{ECO:0000269|PubMed:1850970}.
MUTAGEN 462 462 R->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. {ECO:0000269|PubMed:1324324,
ECO:0000269|PubMed:8254658}.
MUTAGEN 560 566 QRRGGKG->AAAAAAA: Loss of gyrase-mediated
DNA wrapping, nearly complete loss of DNA
supercoiling activity, no change in DNA
supercoil relaxation or DNA decatenation
activity. {ECO:0000269|PubMed:16332690}.
MUTAGEN 560 566 Missing: Loss of gyrase-mediated DNA
wrapping, nearly complete loss of DNA
supercoiling activity, no change in DNA
supercoil relaxation or DNA decatenation
activity. {ECO:0000269|PubMed:16332690}.
MUTAGEN 842 856 Missing: 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.
{ECO:0000269|PubMed:22457352,
ECO:0000269|PubMed:22457353}.
MUTAGEN 854 875 Missing: Isolated CTD gains ability to
wrap DNA around itself in the absence of
GyrB, binds DNA better than wild-type
CTD. {ECO:0000269|PubMed:22457353}.
TURN 31 33 {ECO:0000244|PDB:1AB4}.
TURN 37 39 {ECO:0000244|PDB:1AB4}.
HELIX 43 54 {ECO:0000244|PDB:1AB4}.
STRAND 59 61 {ECO:0000244|PDB:1AB4}.
HELIX 66 76 {ECO:0000244|PDB:1AB4}.
HELIX 82 91 {ECO:0000244|PDB:1AB4}.
TURN 95 97 {ECO:0000244|PDB:1AB4}.
STRAND 102 107 {ECO:0000244|PDB:1AB4}.
TURN 120 122 {ECO:0000244|PDB:1AB4}.
STRAND 124 127 {ECO:0000244|PDB:1AB4}.
HELIX 131 134 {ECO:0000244|PDB:1AB4}.
TURN 136 141 {ECO:0000244|PDB:1AB4}.
STRAND 145 147 {ECO:0000244|PDB:1AB4}.
STRAND 151 158 {ECO:0000244|PDB:1AB4}.
HELIX 165 169 {ECO:0000244|PDB:1AB4}.
STRAND 171 173 {ECO:0000244|PDB:1AB4}.
STRAND 180 182 {ECO:0000244|PDB:1AB4}.
HELIX 187 199 {ECO:0000244|PDB:1AB4}.
HELIX 205 208 {ECO:0000244|PDB:1AB4}.
TURN 209 211 {ECO:0000244|PDB:1AB4}.
HELIX 227 235 {ECO:0000244|PDB:1AB4}.
STRAND 236 243 {ECO:0000244|PDB:1AB4}.
STRAND 245 249 {ECO:0000244|PDB:1AB4}.
STRAND 258 263 {ECO:0000244|PDB:1AB4}.
HELIX 270 281 {ECO:0000244|PDB:1AB4}.
TURN 282 284 {ECO:0000244|PDB:1AB4}.
STRAND 292 294 {ECO:0000244|PDB:1AB4}.
STRAND 298 300 {ECO:0000244|PDB:1AB4}.
STRAND 303 305 {ECO:0000244|PDB:1AB4}.
HELIX 314 323 {ECO:0000244|PDB:1AB4}.
STRAND 327 333 {ECO:0000244|PDB:1AB4}.
STRAND 335 338 {ECO:0000244|PDB:1AB4}.
STRAND 341 344 {ECO:0000244|PDB:1AB4}.
HELIX 347 388 {ECO:0000244|PDB:1AB4}.
HELIX 390 399 {ECO:0000244|PDB:1AB4}.
STRAND 400 402 {ECO:0000244|PDB:1X75}.
HELIX 403 412 {ECO:0000244|PDB:1AB4}.
HELIX 419 421 {ECO:0000244|PDB:1AB4}.
STRAND 441 449 {ECO:0000244|PDB:1AB4}.
HELIX 452 459 {ECO:0000244|PDB:1AB4}.
HELIX 463 466 {ECO:0000244|PDB:1AB4}.
HELIX 468 493 {ECO:0000244|PDB:1AB4}.
HELIX 495 513 {ECO:0000244|PDB:1AB4}.
STRAND 519 521 {ECO:0000244|PDB:1AB4}.
STRAND 538 544 {ECO:0000244|PDB:1ZI0}.
STRAND 547 553 {ECO:0000244|PDB:1ZI0}.
HELIX 556 560 {ECO:0000244|PDB:1ZI0}.
STRAND 578 585 {ECO:0000244|PDB:1ZI0}.
STRAND 589 594 {ECO:0000244|PDB:1ZI0}.
STRAND 597 603 {ECO:0000244|PDB:1ZI0}.
HELIX 604 606 {ECO:0000244|PDB:1ZI0}.
STRAND 612 614 {ECO:0000244|PDB:1ZI0}.
HELIX 619 621 {ECO:0000244|PDB:1ZI0}.
STRAND 631 638 {ECO:0000244|PDB:1ZI0}.
STRAND 645 650 {ECO:0000244|PDB:1ZI0}.
STRAND 653 659 {ECO:0000244|PDB:1ZI0}.
HELIX 660 663 {ECO:0000244|PDB:1ZI0}.
STRAND 671 674 {ECO:0000244|PDB:1ZI0}.
STRAND 682 688 {ECO:0000244|PDB:1ZI0}.
STRAND 693 698 {ECO:0000244|PDB:1ZI0}.
STRAND 701 707 {ECO:0000244|PDB:1ZI0}.
HELIX 708 710 {ECO:0000244|PDB:1ZI0}.
STRAND 732 736 {ECO:0000244|PDB:1ZI0}.
STRAND 743 748 {ECO:0000244|PDB:1ZI0}.
STRAND 751 756 {ECO:0000244|PDB:1ZI0}.
HELIX 758 760 {ECO:0000244|PDB:1ZI0}.
STRAND 771 774 {ECO:0000244|PDB:1ZI0}.
TURN 778 780 {ECO:0000244|PDB:1ZI0}.
STRAND 782 789 {ECO:0000244|PDB:1ZI0}.
STRAND 794 801 {ECO:0000244|PDB:1ZI0}.
STRAND 804 808 {ECO:0000244|PDB:1ZI0}.
HELIX 809 811 {ECO:0000244|PDB:1ZI0}.
STRAND 833 838 {ECO:0000244|PDB:1ZI0}.
SEQUENCE 875 AA; 96964 MW; 3FD5BD52A5969069 CRC64;
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


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