GYRB_PSEPU
ID GYRB_PSEPU Reviewed; 806 AA.
AC P13364;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1991, sequence version 2.
DT 03-AUG-2022, entry version 129.
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};
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PRS2000;
RX PubMed=2170947; DOI=10.1093/nar/18.19.5880;
RA Parales R.E., Harwood C.S.;
RT "Nucleotide sequence of the gyrB gene of Pseudomonas putida.";
RL Nucleic Acids Res. 18:5880-5880(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 128-496.
RC STRAIN=ATCC 33015 / JCM 6156, and PB4;
RX PubMed=7793912; DOI=10.1128/aem.61.3.1104-1109.1995;
RA Yamamoto S., Harayama S.;
RT "PCR amplification and direct sequencing of gyrB genes with universal
RT primers and their application to the detection and taxonomic analysis of
RT Pseudomonas putida strains.";
RL Appl. Environ. Microbiol. 61:1104-1109(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-47.
RC STRAIN=TN2100;
RX PubMed=2540413; DOI=10.1007/bf00427033;
RA Fujita M.Q., Yoshikawa H., Ogasawara N.;
RT "Structure of the dnaA region of Pseudomonas putida: conservation among
RT three bacteria, Bacillus subtilis, Escherichia coli and P. putida.";
RL Mol. Gen. Genet. 215:381-387(1989).
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; X54631; CAA38447.1; -; Genomic_DNA.
DR EMBL; D37926; BAA07144.1; -; Genomic_DNA.
DR EMBL; D37927; BAA07145.1; -; Genomic_DNA.
DR EMBL; X14792; CAA32897.1; -; Genomic_DNA.
DR PIR; S12608; S12608.
DR RefSeq; WP_016497346.1; NZ_WOWR01000057.1.
DR AlphaFoldDB; P13364; -.
DR SMR; P13364; -.
DR STRING; 1240350.AMZE01000066_gene3197; -.
DR PRIDE; P13364; -.
DR GeneID; 45521529; -.
DR eggNOG; COG0187; Bacteria.
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; -; 2.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR041423; GyrB_insert.
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; PF18053; GyrB_insert; 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 Antibiotic resistance; ATP-binding; Cytoplasm; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Topoisomerase.
FT CHAIN 1..806
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145329"
FT DOMAIN 420..535
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 426
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 451
FT /note="Interaction with DNA"
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 VARIANT 161
FT /note="E -> D (in strain: JCM 6156 and PB4)"
FT VARIANT 245
FT /note="S -> N (in strain: JCM 6156 and PB4)"
FT VARIANT 249
FT /note="E -> D (in strain: JCM 6156)"
FT VARIANT 297
FT /note="S -> N (in strain: PB4)"
FT VARIANT 358
FT /note="Y -> F (in strain: PB4)"
FT VARIANT 360
FT /note="S -> A (in strain: JCM 6156 and PB4)"
SQ SEQUENCE 806 AA; 90078 MW; 3A99964341D016C8 CRC64;
MSENQTYDSS SIKVLKGLDA VRKRPGMYIG DTDDGSGLHH MVFEVVDNSI DEALAGHCDD
ITVIIHTDES ISVRDNGRGI PVDVHKEEGV SAAEVIMTVL HAGGKFDDNS YKVSGGLHGV
GVSVVNALSE KLVLTVRRSG KIWEQTYVHG VPQAPMAVVG ESETTGTHIH FKPSAETFKN
IHFSWDILAK RIRELSFLNS GVGILLKDER SGKEEFFKYE GGLRAFVEYL NTNKTPVNSQ
VFHFSVQRED GVGVEVALQW NDSFNENLLC FTNNIPQRDG GTHLVGFRSS LTRSLNSYIE
QEGLAKKNKV ATTGDDAREG LTAIISVKVP DPKFSSQTKD KLVSSEVKTA VEQEMNKYFS
DFLLENPNEA KAVVGKMIDA ARAREAARKA REMTRRKGAL DIAGLPGKLA DCQEKDPALS
ELYLVEGDSA GGSAKQGRNR RTQAILPLKG KILNVEKARF DKMISSQEVG TLITALGCGI
GREEYNIDKL RYHNIIIMTD ADVDGSHIRT LLLTFFFRQL PELVERGYIY IAQPPLYKVK
KGKQEQYIKD DEAMEEYMTQ SALEDASLHL DESAPAVSGV QLESLVNEFR SVMKTLKRLS
RLYPEELTEH FVYLPEVTLE QLGDHAVMQA WLAKLQERLN SSQKSGLAYN ASLREDKERN
VWLPEVEITS HGLASYITFN RDFFGSNDYR TVVNIGAKLS SLLGEGAYVQ RGERRKAIVE
FKEGLDWLMN ETTKRHTIQR YKGLGEMNPD QLWETTMDPT VRRMLKVTIE DAIAADQIFN
TLMGDAVEPR REFIESNALS VSNLDF
