ID   GYRB_CHIJA              Reviewed;         481 AA.
AC   Q9FAX2;
DT   09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2001, sequence version 1.
DT   03-AUG-2022, entry version 80.
DE   RecName: Full=DNA gyrase subunit B;
DE            EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE   Flags: Fragment;
GN   Name=gyrB;
OS   Chitinophaga japonensis (Flexibacter japonensis).
OC   Bacteria; Bacteroidetes; Chitinophagia; Chitinophagales; Chitinophagaceae;
OC   Chitinophaga.
OX   NCBI_TaxID=104662;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=DSM 13484 / JCM 9735 / NBRC 16041;
RA   Suzuki M., Yamaguchi K.;
RT   "Phylogenetic analysis and taxonomic study of marine Cytophaga like
RT   bacteria. Proposal of Haerentibaculum gen. nov. with Haerentibaculum
RT   maritimum comb. nov. and Haerentibaculum ovolyticus comb. nov., and two new
RT   species.";
RL   Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases.
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.
CC       {ECO:0000250|UniProtKB:P0AES6}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP-dependent breakage, passage and rejoining of double-
CC         stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00995};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
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|PROSITE-
CC       ProRule:PRU00995};
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:0000250|UniProtKB:P0AES6}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P0AES6}.
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.
CC       {ECO:0000250|UniProtKB:P0AES6}.
CC   -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC       {ECO:0000305}.
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DR   EMBL; AB032579; BAB13317.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q9FAX2; -.
DR   SMR; Q9FAX2; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006265; P:DNA topological change; IEA:InterPro.
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   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; PF01751; Toprim; 1.
DR   SMART; SM00433; TOP2c; 1.
DR   SUPFAM; SSF54211; SSF54211; 1.
DR   SUPFAM; SSF55874; SSF55874; 1.
DR   SUPFAM; SSF56719; SSF56719; 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; Topoisomerase.
FT   CHAIN           <1..>481
FT                   /note="DNA gyrase subunit B"
FT                   /id="PRO_0000145312"
FT   DOMAIN          323..442
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         329
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         407
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         407
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         409
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            354
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            357
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   NON_TER         1
FT   NON_TER         481
SQ   SEQUENCE   481 AA;  53557 MW;  8707FEA30BDA70B1 CRC64;
     DKNTYKVSGG LHGVGVSCVN ALSTVLHVTV HREGKIFEQE YHRGVPQYAV REIGATTDTG
     TTTHFKPDGE IFTETSYNRE ILAGRLRELA YLNRKIRITL TDEREKDEQG NVLSEPFYSE
     GGIMEFVQML DRNGRRNSLL PAPIFIEAHD APSNVAVEVS LQYNDSFSEN IFSYVNNINT
     IEGGTHVAGF RRAITRVFKT YGDRNKLFEK SKIEVTGDDF REGLSAIVSV KVPEPQFEGQ
     TKTKLGNSDV MGVVDSAVAD VLNAYLEEHP KEARTVINKV VLAAQAREAA RKARQLVQRK
     SVLTGSGLPG KLADCSENDP EKCELYLVEG DSAGGTAKQG RNRAFQAILP LRGKILNVEK
     AMEHKIYENE EIKNIFTALG VTIGTEEDDK ALNLSKLRYH KLIIMTDADV DGSHIATLIL
     TFVFRYMKAL VEQGYVYIAQ PPLYLVKKGK EQIYAWTEEQ RKAAVATLAG GKEDSVTIQR
     Y