GYRB_HALL2
ID GYRB_HALL2 Reviewed; 639 AA.
AC P21558; M0GQM6;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 14-MAY-2014, 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}; ORFNames=C456_09163;
OS Haloferax lucentense (strain DSM 14919 / JCM 9276 / NCIMB 13854 / Aa 2.2)
OS (Haloferax alicantei).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales;
OC Haloferacaceae; Haloferax.
OX NCBI_TaxID=1230452;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF MUTANT NOVR, INDUCTION, ANTIBIOTIC
RP RESISTANCE, AND MUTAGENESIS OF ASP-82; SER-122 AND ARG-137.
RC STRAIN=DSM 14919 / CCM 7023 / CIP 107410 / JCM 9276 / NCIMB 13854 / Aa 2.2;
RX PubMed=1846146; DOI=10.1128/jb.173.2.642-648.1991;
RA Holmes M.L., Dyall-Smith M.L.;
RT "Mutations in DNA gyrase result in novobiocin resistance in halophilic
RT archaebacteria.";
RL J. Bacteriol. 173:642-648(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14919 / CCM 7023 / CIP 107410 / JCM 9276 / NCIMB 13854 / Aa 2.2;
RX PubMed=25393412; DOI=10.1371/journal.pgen.1004784;
RA Becker E.A., Seitzer P.M., Tritt A., Larsen D., Krusor M., Yao A.I., Wu D.,
RA Madern D., Eisen J.A., Darling A.E., Facciotti M.T.;
RT "Phylogenetically driven sequencing of extremely halophilic archaea reveals
RT strategies for static and dynamic osmo-response.";
RL PLoS Genet. 10:E1004784-E1004784(2014).
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 -!- INDUCTION: Expressed in mid-log phase; not induced by novobiocin.
CC {ECO:0000269|PubMed:1846146}.
CC -!- MISCELLANEOUS: Novobiocin inhibits DNA gyrase activity by binding to
CC GyrB and blocking access of ATP to its binding site on this subunit.
CC The mutations in GyrB causing novobiocin-resistance probably produce a
CC gyrase that binds novobiocin less avidly.
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; M38373; AAB09605.1; -; Genomic_DNA.
DR EMBL; AOLH01000015; ELZ74526.1; -; Genomic_DNA.
DR RefSeq; WP_004063239.1; NZ_AOLH01000015.1.
DR AlphaFoldDB; P21558; -.
DR SMR; P21558; -.
DR PRIDE; P21558; -.
DR EnsemblBacteria; ELZ74526; ELZ74526; C456_09163.
DR GeneID; 44083938; -.
DR PATRIC; fig|1230452.3.peg.1758; -.
DR Proteomes; UP000011535; Unassembled WGS sequence.
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 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; -; 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 1: Evidence at protein level;
KW Antibiotic resistance; ATP-binding; Cytoplasm; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Topoisomerase.
FT CHAIN 1..639
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145361"
FT DOMAIN 423..537
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 392..417
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 429
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 502
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 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 504
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 454
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 457
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT MUTAGEN 82
FT /note="D->G: In Nov(r); Allows cells to grow in about 1000
FT times higher novobiocin concentrations; when associated
FT with T-122 and H-137."
FT /evidence="ECO:0000269|PubMed:1846146"
FT MUTAGEN 122
FT /note="S->T: In Nov(r); Allows cells to grow in about 1000
FT times higher novobiocin concentrations; when associated
FT with G-82 and H-137."
FT /evidence="ECO:0000269|PubMed:1846146"
FT MUTAGEN 137
FT /note="R->H: In Nov(r); Allows cells to grow in about 1000
FT times higher novobiocin concentrations; when associated
FT with G-82 and T-122."
FT /evidence="ECO:0000269|PubMed:1846146"
SQ SEQUENCE 639 AA; 71201 MW; EE2327072C5F3E66 CRC64;
MSQDNEYGAG QIQVLEGLEA VRKRPAMYIG STDSRGLHHL VYEVVDNSID EALAGHCDAI
EVALHEDGSV SVTDNGRGIP VDTHEQYDRP ALEVIMTVLH AGGKFDNKSY QVSGGLHGVG
VSVVNALSSE LEVEVKRDGA VWTHRFEVGE PQVEEFERVR DLEPGEDTGT TIRFWPDDGI
FETTEFDFKT LENRLRELAF LNSGVEISLS DERTDESSTF LFEGGIREFV EYLNETKTAL
HDDVIYYDDE SEGIEVEIAM QATDELQGSI HAFANNINTR EGGTHLTGFK TALTRVVNDY
ANSHDMLDDL DGDNLRGEDV REGLTAVISV KHPDPQFEGQ TKTKLGNSEV RGIVESVTHQ
QLGTFFEENP DTATAIISKA VEAARARKAA KQAEELTRRK SALESTSLPG KLADCQSRDP
SESELFIVEG DSAGGSAKQG RDRKFQAILP LKGKILNVEK HRLDRILEND EIRALITAIG
GGVGDEFDIE KARYQRLILM TDADVDGAHI RTLLLTLLYR HMRPLIEAGY VYAAQPPLYR
VRYRGNTYDA MDEAERDRII EEECNGNPTQ VQRFKGLGEM NPDQLWDTTM NPENRVLKRI
TVEDAAAADR MFNILMGDAV GPRKQFIKDH ANDAEWVDI
