GYRB_ALKHC
ID GYRB_ALKHC Reviewed; 637 AA.
AC O50627; Q9JPZ1;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 131.
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=BH0006;
OS Alkalihalobacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344
OS / JCM 9153 / C-125) (Bacillus halodurans).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Alkalihalobacillus.
OX NCBI_TaxID=272558;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125;
RA Masui N., Nakasone K., Horikoshi K.;
RT "Cloning and expression of the genes encoding DNA gyrase from alkaliphilic
RT Bacillus sp. strain C-125.";
RL Submitted (DEC-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125;
RX PubMed=10427704; DOI=10.1271/bbb.63.1134;
RA Takami H., Masui N., Nakasone K., Horikoshi K.;
RT "Replication origin region of the chromosome of alkaliphilic Bacillus
RT halodurans C-125.";
RL Biosci. Biotechnol. Biochem. 63:1134-1137(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125;
RX PubMed=11058132; DOI=10.1093/nar/28.21.4317;
RA Takami H., Nakasone K., Takaki Y., Maeno G., Sasaki R., Masui N., Fuji F.,
RA Hirama C., Nakamura Y., Ogasawara N., Kuhara S., Horikoshi K.;
RT "Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans
RT and genomic sequence comparison with Bacillus subtilis.";
RL Nucleic Acids Res. 28:4317-4331(2000).
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; AB010081; BAA24187.1; -; Genomic_DNA.
DR EMBL; AB013492; BAA82690.1; -; Genomic_DNA.
DR EMBL; BA000004; BAB03725.1; -; Genomic_DNA.
DR PIR; F83650; F83650.
DR PIR; T46551; T46551.
DR RefSeq; WP_010896190.1; NC_002570.2.
DR AlphaFoldDB; O50627; -.
DR SMR; O50627; -.
DR STRING; 272558.10172618; -.
DR EnsemblBacteria; BAB03725; BAB03725; BAB03725.
DR KEGG; bha:BH0006; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_1_2_9; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000001258; 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; -; 1.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
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; 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 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..637
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145292"
FT DOMAIN 421..535
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 427
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 500
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 500
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
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 SITE 455
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 637 AA; 71233 MW; CB5A32A3817B67F7 CRC64;
MTREQQAYDE SQIQVLEGLE AVRKRPGMYI GSTSSRGLHH LVWEIVDNSI DEAMAGFCDE
IGVVIEEDNS ITVTDNGRGI PVGIHEKMGR PAVEVIMTVL HAGGKFGGGG YKVSGGLHGV
GASVVNALST MLEVEVHREG KVHYQKFHRG VPAADLEVIG TTDRTGTKIH FKPDGDIFTE
TTVFEYDTLA SRLRELAFLN KGLRIKITDM REEEKSDEFH YEGGIASFVE HLNRTRETLH
ETPIHIEGEK QGVYVEIAVQ YNDGFTSNIY SFANNINTHE GGTHESGFKT GLTRVINDYA
RKHNLFKESD PNLTGEDVRE GLTAIISVKI PDPQFEGQTK TKLGNSEART ITDSLFTEHF
SRFLIEHPQV ARKLVDKGLM ASRAREAAKK ARELTRRKSA LEVSSLPGKL ADCSSRDASI
SEIYIVEGDS AGGSAKQGRD RHFQAILPLR GKILNVEKAR LDKILANNEI RAIITALGTG
IGDDFDIEKA RYHKIIIMTD ADVDGAHIRT LILTFFYRYM RPLIEHGYVY IAQPPLYKVQ
QGKDIQYAYG DAELQEILSQ LPDKAKPGIQ RYKGLGEMNP SQLWETTMDP GQRTVLQVTL
EDAMKADEIF EILMGDRVEP RRDFIQENAR YVKNLDI
