GYRB_BACMY
ID GYRB_BACMY Reviewed; 404 AA.
AC Q9X3Y5;
DT 24-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 89.
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 Bacillus mycoides.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1405;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 6462 / DSM 2048 / CCUG 26678 / LMG 7128 / NCTC 12974 / NRS 273;
RX PubMed=10103241; DOI=10.1128/aem.65.4.1483-1490.1999;
RA Yamada S., Ohashi E., Agata N., Venkateswaran K.;
RT "Cloning and nucleotide sequence analysis of gyrB of Bacillus cereus, B.
RT thuringiensis, B. mycoides, and B. anthracis and their application to the
RT detection of B. cereus in rice.";
RL Appl. Environ. Microbiol. 65:1483-1490(1999).
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; AF090332; AAD25957.1; -; Genomic_DNA.
DR AlphaFoldDB; Q9X3Y5; -.
DR SMR; Q9X3Y5; -.
DR STRING; 1405.DJ92_2588; -.
DR eggNOG; COG0187; Bacteria.
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 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 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..>404
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145293"
FT DOMAIN 321..>404
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 327
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 400
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 400
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 402
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 352
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 355
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT NON_TER 1
FT NON_TER 404
SQ SEQUENCE 404 AA; 44896 MW; 44E9F79C88F627E9 CRC64;
HAGGKFDGGG YKVSGGLHGV GASVVNALST ELEVFVHRDG KIHYQKYERG VPAADLRVIG
ETDRTGTITR FKPDSEIFTE TTEYEFDTLA TRMRELAFLN RNIKLTIEDK REHKQKKEFH
YEGGIKSYVE HLNRSKQPIH EEPVYVDGSK DGIQVEVALQ YNEGYTNHIY SFTNNIHTYE
GGTHEVGFKT ALTRVINDYG RKNNILKDAD SNLTGEDVRE GLTAIVSIKH PNPQFEGQTK
TKLGNSEART ITESVFSEAF EKFLLENPNV ARKIIDKGTM AARARVAAKK ARELTRRKSA
LEVSSLPGKL ADCSSKDPAI SEIYIVEGDS AGGSAKQGRD RHFQAILPLK GKIINVEKAR
LDKILSNDEV RTIITAIGTN IGGDFAIEKA RYHKVIIMTD ADVD
