GYRB_SALTI
ID GYRB_SALTI Reviewed; 804 AA.
AC P0A2I4; P77981; P77982; Q60008;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898};
GN OrderedLocusNames=STY3943, t3684;
OS Salmonella typhi.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=90370;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CT18;
RX PubMed=11677608; DOI=10.1038/35101607;
RA Parkhill J., Dougan G., James K.D., Thomson N.R., Pickard D., Wain J.,
RA Churcher C.M., Mungall K.L., Bentley S.D., Holden M.T.G., Sebaihia M.,
RA Baker S., Basham D., Brooks K., Chillingworth T., Connerton P., Cronin A.,
RA Davis P., Davies R.M., Dowd L., White N., Farrar J., Feltwell T.,
RA Hamlin N., Haque A., Hien T.T., Holroyd S., Jagels K., Krogh A.,
RA Larsen T.S., Leather S., Moule S., O'Gaora P., Parry C., Quail M.A.,
RA Rutherford K.M., Simmonds M., Skelton J., Stevens K., Whitehead S.,
RA Barrell B.G.;
RT "Complete genome sequence of a multiple drug resistant Salmonella enterica
RT serovar Typhi CT18.";
RL Nature 413:848-852(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700931 / Ty2;
RX PubMed=12644504; DOI=10.1128/jb.185.7.2330-2337.2003;
RA Deng W., Liou S.-R., Plunkett G. III, Mayhew G.F., Rose D.J., Burland V.,
RA Kodoyianni V., Schwartz D.C., Blattner F.R.;
RT "Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and
RT CT18.";
RL J. Bacteriol. 185:2330-2337(2003).
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 Negative supercoiling favors strand separation, and DNA replication,
CC transcription, recombination and repair, all of which involve strand
CC separation. Also able to catalyze the interconversion of other
CC topological isomers of dsDNA rings, including catenanes and knotted
CC rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC Rule:MF_01898}.
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_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-Rule:MF_01898};
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_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
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_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; AL513382; CAD03160.1; -; Genomic_DNA.
DR EMBL; AE014613; AAO71180.1; -; Genomic_DNA.
DR RefSeq; NP_458107.1; NC_003198.1.
DR RefSeq; WP_000072047.1; NZ_WSUR01000023.1.
DR PDB; 6J90; X-ray; 2.20 A; A=1-394.
DR PDBsum; 6J90; -.
DR AlphaFoldDB; P0A2I4; -.
DR SMR; P0A2I4; -.
DR STRING; 220341.16504795; -.
DR PRIDE; P0A2I4; -.
DR EnsemblBacteria; AAO71180; AAO71180; t3684.
DR KEGG; stt:t3684; -.
DR KEGG; sty:STY3943; -.
DR PATRIC; fig|220341.7.peg.4025; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_6; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000000541; Chromosome.
DR Proteomes; UP000002670; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR041423; GyrB_insert.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034160; TOPRIM_GyrB.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF18053; GyrB_insert; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..804
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145333"
FT DOMAIN 418..533
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 424
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 498
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 498
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 500
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 449
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 452
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 17..21
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 23..26
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 34..52
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:6J90"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 90..96
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 119..125
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 127..136
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 139..146
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 164..171
FT /evidence="ECO:0007829|PDB:6J90"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 184..197
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 202..207
FT /evidence="ECO:0007829|PDB:6J90"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 221..230
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 241..247
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 250..262
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 265..270
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 280..299
FT /evidence="ECO:0007829|PDB:6J90"
FT TURN 300..302
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 303..308
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 312..316
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 319..326
FT /evidence="ECO:0007829|PDB:6J90"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 344..363
FT /evidence="ECO:0007829|PDB:6J90"
FT HELIX 365..392
FT /evidence="ECO:0007829|PDB:6J90"
SQ SEQUENCE 804 AA; 89896 MW; BC984F67483751B1 CRC64;
MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKDIV
VTIHADNSVS VTDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
SVVNALSQKL ELVIQRDGKI HRQIYEHGVP QAPLAVTGDT DKTGTMVRFW PSHETFTNVT
EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI
FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE
GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLSEY
LLENPSDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL
YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR
DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG
KQEQYIKDDE AMDQYQISIA LDGATLHANA HAPALSGEAL EKLVSEYNAT QKMIGRMERR
FPKALLKELV YQPTLTEADL SDEQTVTRWV NALITELNEK EQHGSQWKFD VHTNTEQNLF
EPIVRVRTHG VDTDYPLDHE FVTGAEYRRI CTLGEKLRGL IEEDAFIERG ERRQPVTSFE
QALEWLVKES RRGLAIQRYK GLGEMNPDQL WETTMDPESR RMLRVTVKDA IAADQLFTTL
MGDAVEPRRA FIEENALKAA NIDI
