GYRB_SALTY
ID GYRB_SALTY Reviewed; 804 AA.
AC P0A2I3; 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 113.
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}; OrderedLocusNames=STM3835;
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 [GENOMIC DNA], AND VARIANT QUINOLONE RESISTANT PHE-464.
RC STRAIN=Copenhagen 685/89, and Copenhagen 80190;
RA Kratz B., Heisig P., Finklenburg B., Ludwig M.;
RL Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases.
RN [2]
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 [3]
RP FUNCTION, AND MUTAGENESIS OF ARG-436.
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=16267301; DOI=10.1128/jb.187.22.7773-7783.2005;
RA Pang Z., Chen R., Manna D., Higgins N.P.;
RT "A gyrase mutant with low activity disrupts supercoiling at the replication
RT terminus.";
RL J. Bacteriol. 187:7773-7783(2005).
RN [4]
RP FUNCTION, AND MUTAGENESIS OF ARG-436.
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 [5]
RP FUNCTION, AND MUTAGENESIS OF CYS-56 AND ARG-436.
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 (PubMed:16267301). Replenishes negative supercoiling downstream of
CC highly transcribed genes to help control overall chromosomal
CC supercoiling density (PubMed:22916023). E.coli makes 15% more negative
CC supercoils in pBR322 plasmid DNA than S.typhimurium; the S.typhimurium
CC GyrB subunit is toxic in E.coli, while the E.coli copy can be expressed
CC in S.typhimurium even though the 2 subunits have 777/804 residues
CC identical (PubMed:17400739). {ECO:0000269|PubMed:16267301,
CC ECO:0000269|PubMed:17400739, 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_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; Y07916; CAA69221.1; -; Genomic_DNA.
DR EMBL; Y08383; CAA69665.1; -; Genomic_DNA.
DR EMBL; Z68167; CAA92320.1; -; Genomic_DNA.
DR EMBL; AE006468; AAL22694.1; -; Genomic_DNA.
DR RefSeq; NP_462735.1; NC_003197.2.
DR RefSeq; WP_000072047.1; NC_003197.2.
DR AlphaFoldDB; P0A2I3; -.
DR SMR; P0A2I3; -.
DR STRING; 99287.STM3835; -.
DR PaxDb; P0A2I3; -.
DR EnsemblBacteria; AAL22694; AAL22694; STM3835.
DR GeneID; 1255362; -.
DR KEGG; stm:STM3835; -.
DR PATRIC; fig|99287.12.peg.4062; -.
DR HOGENOM; CLU_006146_4_1_6; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; P0A2I3; -.
DR BioCyc; SENT99287:STM3835-MON; -.
DR Proteomes; UP000001014; 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; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
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 Antibiotic resistance; ATP-binding; Cytoplasm; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome;
KW 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_0000145334"
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 VARIANT 464
FT /note="S -> F (in strain: 80190; quinolone-resistant)"
FT /evidence="ECO:0000269|Ref.1"
FT MUTAGEN 56
FT /note="C->Y: In gyrB1820TS; a temperature-sensitive mutant,
FT 50% decreased growth rate, greatly decreased (-)
FT supercoiling even at permissive temperature."
FT /evidence="ECO:0000269|PubMed:22916023"
FT MUTAGEN 436
FT /note="R->S: In gyrB652TS; a temperature-sensitive mutant,
FT no growth at 42 degrees Celsius, 36% decreased growth rate
FT at 30 degrees Celsius (permissive), low k(cat) at 30, 37
FT and 42 degrees Celsius, in vivo significantly decreased (-)
FT supercoiling even at permissive temperature."
FT /evidence="ECO:0000269|PubMed:16267301,
FT ECO:0000269|PubMed:22916023"
FT CONFLICT 358
FT /note="S -> A (in Ref. 1; CAA69221/CAA69665)"
FT /evidence="ECO:0000305"
FT CONFLICT 366
FT /note="S -> T (in Ref. 1; CAA69221/CAA69665)"
FT /evidence="ECO:0000305"
FT CONFLICT 568
FT /note="A -> T (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 571
FT /note="H -> S (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 576
FT /note="S -> A (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 595
FT /note="G -> N (in Ref. 1; CAA69221/CAA69665)"
FT /evidence="ECO:0000305"
FT CONFLICT 601
FT /note="F -> Y (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 605
FT /note="L -> M (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 610
FT /note="V -> I (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 634..635
FT /note="IT -> VS (in Ref. 1; CAA69221/CAA69665)"
FT /evidence="ECO:0000305"
FT CONFLICT 639
FT /note="E -> D (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 655
FT /note="T -> A (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 682
FT /note="V -> I (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 685
FT /note="A -> G (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 701
FT /note="I -> L (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 717
FT /note="T -> A (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 724
FT /note="E -> D (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 735
FT /note="A -> S (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
FT CONFLICT 748
FT /note="D -> E (in Ref. 1; CAA69221/CAA69665/CAA92320)"
FT /evidence="ECO:0000305"
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
