GYRA_SALTY
ID GYRA_SALTY Reviewed; 878 AA.
AC P37411;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 13-DEC-2001, sequence version 3.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DNA gyrase subunit A {ECO:0000255|HAMAP-Rule:MF_01897};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01897};
GN Name=gyrA {ECO:0000255|HAMAP-Rule:MF_01897}; OrderedLocusNames=STM2272;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 39-160.
RC STRAIN=NCTC 74;
RA Griggs D.J.;
RL Submitted (FEB-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 72-166.
RC STRAIN=SM4;
RA Ruiz J., Castro D., Goni P., Borrego J.J., Vila J.;
RL Submitted (MAY-1995) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 74-159.
RC STRAIN=NCTC 74;
RX PubMed=8849216; DOI=10.1128/aac.40.4.1009;
RA Griggs D., Gensberg K., Piddock L.J.V.;
RT "Mutations in gyrA gene of quinolone-resistant Salmonella serotypes
RT isolated from humans and animals.";
RL Antimicrob. Agents Chemother. 40:1009-1013(1996).
RN [5]
RP FUNCTION.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=17400739; DOI=10.1128/jb.00083-07;
RA Champion K., Higgins N.P.;
RT "Growth rate toxicity phenotypes and homeostatic supercoil control
RT differentiate Escherichia coli from Salmonella enterica serovar
RT Typhimurium.";
RL J. Bacteriol. 189:5839-5849(2007).
RN [6]
RP FUNCTION, AND MUTAGENESIS OF ARG-358 AND GLY-597.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=22916023; DOI=10.1371/journal.pgen.1002845;
RA Rovinskiy N., Agbleke A.A., Chesnokova O., Pang Z., Higgins N.P.;
RT "Rates of gyrase supercoiling and transcription elongation control
RT supercoil density in a bacterial chromosome.";
RL PLoS Genet. 8:E1002845-E1002845(2012).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner to
CC modulate DNA topology and maintain chromosomes in an underwound state,
CC and also catalyzes the interconversion of other topological isomers of
CC double-stranded DNA rings, including catenanes and knotted rings.
CC Replenishes negative supercoiling downstream of highly transcribed
CC genes to help control overall chromosomal supercoiling density
CC (PubMed:22916023). E.coli makes 15% more negative supercoils in pBR322
CC plasmid DNA than S.typhimurium; the S.typhimurium GyrB subunit is toxic
CC in E.coli, while the E.coli copy can be expressed in S.typhimurium even
CC though the 2 subunits have 777/804 residues identical
CC (PubMed:17400739). {ECO:0000269|PubMed:17400739,
CC ECO:0000269|PubMed:22916023}.
CC -!- FUNCTION: Negative supercoiling favors strand separation, and DNA
CC replication, transcription, recombination and repair, all of which
CC involve strand separation. Type II topoisomerases break and join 2 DNA
CC strands simultaneously in an ATP-dependent manner.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01897};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In
CC the heterotetramer, GyrA contains the active site tyrosine that forms a
CC transient covalent intermediate with DNA, while GyrB binds cofactors
CC and catalyzes ATP hydrolysis. {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01897}.
CC -!- MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming
CC negative supercoils. Not all organisms have 2 type II topoisomerases;
CC in organisms with a single type II topoisomerase this enzyme also has
CC to decatenate newly replicated chromosomes. {ECO:0000255|HAMAP-
CC Rule:MF_01897}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrA/ParC subunit
CC family. {ECO:0000255|HAMAP-Rule:MF_01897}.
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DR EMBL; AE006468; AAL21173.1; -; Genomic_DNA.
DR EMBL; X78977; CAA55580.1; -; Genomic_DNA.
DR EMBL; X86695; CAA60388.1; -; Genomic_DNA.
DR PIR; S54254; S54254.
DR RefSeq; NP_461214.1; NC_003197.2.
DR RefSeq; WP_001281271.1; NC_003197.2.
DR AlphaFoldDB; P37411; -.
DR SMR; P37411; -.
DR STRING; 99287.STM2272; -.
DR PaxDb; P37411; -.
DR EnsemblBacteria; AAL21173; AAL21173; STM2272.
DR GeneID; 1253794; -.
DR KEGG; stm:STM2272; -.
DR PATRIC; fig|99287.12.peg.2405; -.
DR HOGENOM; CLU_002977_6_1_6; -.
DR OMA; THHWLLF; -.
DR PhylomeDB; P37411; -.
DR BioCyc; SENT99287:STM2272-MON; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0009330; C:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0034335; F:DNA negative supercoiling activity; IEA:UniProt.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd00187; TOP4c; 1.
DR Gene3D; 1.10.268.10; -; 1.
DR Gene3D; 2.120.10.90; -; 1.
DR Gene3D; 3.90.199.10; -; 1.
DR HAMAP; MF_01897; GyrA; 1.
DR InterPro; IPR005743; GyrA.
DR InterPro; IPR006691; GyrA/parC_rep.
DR InterPro; IPR035516; Gyrase/topoIV_suA_C.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013758; Topo_IIA_A/C_ab.
DR InterPro; IPR013757; Topo_IIA_A_a_sf.
DR InterPro; IPR002205; Topo_IIA_dom_A.
DR Pfam; PF03989; DNA_gyraseA_C; 6.
DR Pfam; PF00521; DNA_topoisoIV; 1.
DR SMART; SM00434; TOP4c; 1.
DR SUPFAM; SSF101904; SSF101904; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Nucleotide-binding;
KW Reference proteome; Topoisomerase.
FT CHAIN 1..878
FT /note="DNA gyrase subunit A"
FT /id="PRO_0000145248"
FT REGION 844..878
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 560..566
FT /note="GyrA-box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT COMPBIAS 845..878
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 122
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01897"
FT MUTAGEN 358
FT /note="R->H: In gyrA213TS; a temperature-sensitive mutant,
FT decreased (-) supercoiling even at permissive temperature."
FT /evidence="ECO:0000269|PubMed:22916023"
FT MUTAGEN 597
FT /note="G->D: In gyrA209TS; a temperature-sensitive mutant,
FT 15% decreased growth rate, decreased (-) supercoiling even
FT at permissive temperature."
FT /evidence="ECO:0000269|PubMed:22916023"
SQ SEQUENCE 878 AA; 97064 MW; CD6F5582190AE53C CRC64;
MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN
KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM
RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT
NIPPHNLTEV INGCLAYIDN EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV
YIRARAEVEA DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKDKRVEGIS ALRDESDKDG
MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI ISAFVRHRRE
VVTRRTIFEL RKARDRAHIL EALAIALANI DPIIELIRRA PTPAEAKAAL ISRPWDLGNV
AAMLERAGDD AARPEWLEPE FGVRDGQYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE
LLEQIAELLH ILGSADRLME VIREEMELIR DQFGDERRTE ITANSADINI EDLISQEDVV
VTLSHQGYVK YQPLTDYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDTI LCFSSRGRLY
WMKVYQLPEA SRGARGRPIV NLLPLEANER ITAILPVREY EEGVNVFMAT ASGTVKKTAL
TEFSRPRSAG IIAVNLNDGD ELIGVDLTSG SDEVMLFSAA GKVVRFKEDA VRAMGRTATG
VRGIKLAGDD KVVSLIIPRG EGAILTVTQN GYGKRTAADE YPTKSRATQG VISIKVTERN
GSVVGAVQVD DCDQIMMITD AGTLVRTRVS EISVVGRNTQ GVILIRTAED ENVVGLQRVA
EPVDDEELDA IDGSVAEGDE DIAPEAESDD DVADDADE
