ID A0A1L7CIX3_CORFL Unreviewed; 694 AA.
AC A0A1L7CIX3;
DT 15-MAR-2017, integrated into UniProtKB/TrEMBL.
DT 15-MAR-2017, sequence version 1.
DT 24-JAN-2024, entry version 33.
DE RecName: Full=DNA gyrase subunit B {ECO:0000256|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000256|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN ECO:0000313|EMBL:KAA8719586.1};
GN ORFNames=CFLV_00025 {ECO:0000313|EMBL:APT85759.1}, F4V60_12415
GN {ECO:0000313|EMBL:KAA8719586.1};
OS Corynebacterium flavescens.
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales;
OC Corynebacteriaceae; Corynebacterium.
OX NCBI_TaxID=28028 {ECO:0000313|EMBL:APT85759.1, ECO:0000313|Proteomes:UP000185479};
RN [1] {ECO:0000313|EMBL:APT85759.1, ECO:0000313|Proteomes:UP000185479}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=OJ8 {ECO:0000313|EMBL:APT85759.1,
RC ECO:0000313|Proteomes:UP000185479};
RA Ruckert C., Albersmeier A., Winkler A., Kalinowski J.;
RT "Complete genome sequence of Corynebacterium flavescens OJ8(T)(=DSM
RT 20296(T)), isolated from cheese.";
RL Submitted (AUG-2014) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KAA8719586.1, ECO:0000313|Proteomes:UP000322697}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCUG 28791T {ECO:0000313|EMBL:KAA8719586.1,
RC ECO:0000313|Proteomes:UP000322697};
RA Pineiro-Iglesias B., Tunovic T., Unosson C., Inganas E., Ohlen M.,
RA Cardew S., Jensie-Markopoulos S., Salva-Serra F., Jaen-Luchoro D.,
RA Karlsson R., Svensson-Stadler L., Chun J., Moore E.;
RT "Draft genome sequence of various Type strains from the CCUG.";
RL Submitted (SEP-2019) 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. {ECO:0000256|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:0000256|ARBA:ARBA00000185,
CC ECO:0000256|HAMAP-Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|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:0000256|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000256|ARBA:ARBA00010708, ECO:0000256|HAMAP-Rule:MF_01898}.
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DR EMBL; CP009246; APT85759.1; -; Genomic_DNA.
DR EMBL; VXKK01000046; KAA8719586.1; -; Genomic_DNA.
DR RefSeq; WP_075728771.1; NZ_VXKK01000046.1.
DR AlphaFoldDB; A0A1L7CIX3; -.
DR STRING; 28028.CFLV_00025; -.
DR GeneID; 82879124; -.
DR KEGG; cfc:CFLV_00025; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000185479; Chromosome.
DR Proteomes; UP000322697; 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:0034335; F:DNA negative supercoiling activity; IEA:UniProt.
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; cd16928; HATPase_GyrB-like; 1.
DR CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
DR Gene3D; 3.30.565.10; Histidine kinase-like ATPase, C-terminal domain; 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_Su5_D2-typ_SF.
DR InterPro; IPR014721; Ribsml_uS5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR000565; Topo_IIA_B.
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 NCBIfam; TIGR01059; gyrB; 1.
DR PANTHER; PTHR45866:SF1; DNA GYRASE SUBUNIT B, MITOCHONDRIAL; 1.
DR PANTHER; PTHR45866; DNA GYRASE/TOPOISOMERASE SUBUNIT B; 1.
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 PRINTS; PR01159; DNAGYRASEB.
DR PRINTS; PR00418; TPI2FAMILY.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase; 1.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
DR SUPFAM; SSF56719; Type II DNA topoisomerase; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01898};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01898};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01898};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Reference proteome {ECO:0000313|Proteomes:UP000185479};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 472..586
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 220..258
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 478
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 551
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 551
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 553
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 503
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 506
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 694 AA; 76335 MW; 2F0813FB583E071E CRC64;
MAEQHAYDAG SITILEGLEA VRKRPGMYIG STGVRGLHHL IWEVVDNSVD EAMAGFASKV
TVKLLADGGV EVIDDGRGIP VEMHASGAPT VQVVMTQLHA GGKFDSDSYA VSGGLHGVGI
SVVNALSTRV EAEIKRDGKH WYQNFSNAIP EDLVEGGNAR GTGTIIRFWA DPEIFETTEY
DFKVISRRLQ EMAFLNKGLT IELIDERVTR EQLELEAIAD AESGETTLDA ESFDDTDGSA
GVDPDASADL STGAPEAKKS GKKLQKKITF YYPDGLIDYV KFLNKSKTPI HPTIVAFDAK
GEEHEVEVAM QWNQGYKESV HTFANTINTY EGGTHEEGFR AALTSLMNRY AKEHKLIKEK
DGNLSGDDCR EGLAAVISVK VGDPQFEGQT KTKLGNSEIK GFVQRAVNEH VNDWFDANPA
EAKAIINKAV SSAHARMAAR KAREMVRRKS ATDLGGLPGK LADCRSKDPK ISELYIVEGD
SAGGSAKGGR DSMFQAILPL RGKILNVEKA RMDKVLKNAE VQAIITALGT GIHEEFDIKK
LRYDKIVLMA DADVDGQHIA TLLLTLLFRF MPQLVEDGHV YLANPPLYKL KWGKGEPGFA
YSDEERDQLL AEGLAENRKI NKDDGIQRYK GLGEMNSSEL WETTLDPASR ILRRVDLEDA
QRADELFSIL MGDDVSARRS FITRRAKDVR FLDV
//
