GYRB_ENTFA
ID GYRB_ENTFA Reviewed; 642 AA.
AC Q839Z1;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 138.
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}; OrderedLocusNames=EF_0005;
OS Enterococcus faecalis (strain ATCC 700802 / V583).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
OC Enterococcus.
OX NCBI_TaxID=226185;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700802 / V583;
RX PubMed=12663927; DOI=10.1126/science.1080613;
RA Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R.,
RA Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H.,
RA Dodson R.J., Umayam L.A., Brinkac L.M., Beanan M.J., Daugherty S.C.,
RA DeBoy R.T., Durkin S.A., Kolonay J.F., Madupu R., Nelson W.C.,
RA Vamathevan J.J., Tran B., Upton J., Hansen T., Shetty J., Khouri H.M.,
RA Utterback T.R., Radune D., Ketchum K.A., Dougherty B.A., Fraser C.M.;
RT "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus
RT faecalis.";
RL Science 299:2071-2074(2003).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 18-224 IN COMPLEX WITH
RP INHIBITORS, FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=23352267; DOI=10.1016/j.bmcl.2012.11.032;
RA Tari L.W., Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J.,
RA Creighton C.J., Cunningham M.L., Kwan B., Stidham M., Shaw K.J.,
RA Lightstone F.C., Wong S.E., Nguyen T.B., Nix J., Finn J.;
RT "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV
RT (ParE). Part I: Structure guided discovery and optimization of dual
RT targeting agents with potent, broad-spectrum enzymatic activity.";
RL Bioorg. Med. Chem. Lett. 23:1529-1536(2013).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) OF 18-224 IN COMPLEX WITH
RP INHIBITORS, FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=24386374; DOI=10.1371/journal.pone.0084409;
RA Tari L.W., Li X., Trzoss M., Bensen D.C., Chen Z., Lam T., Zhang J.,
RA Lee S.J., Hough G., Phillipson D., Akers-Rodriguez S., Cunningham M.L.,
RA Kwan B.P., Nelson K.J., Castellano A., Locke J.B., Brown-Driver V.,
RA Murphy T.M., Ong V.S., Pillar C.M., Shinabarger D.L., Nix J.,
RA Lightstone F.C., Wong S.E., Nguyen T.B., Shaw K.J., Finn J.;
RT "Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum
RT dual-targeting antibacterial agents.";
RL PLoS ONE 8:E84409-E84409(2013).
CC -!- FUNCTION: DNA gyrase negatively supercoils closed circular double-
CC stranded DNA in an ATP-dependent manner and also catalyzes the
CC interconversion of other topological isomers of double-stranded DNA
CC rings, including catenanes and knotted rings. {ECO:0000255|HAMAP-
CC Rule:MF_01898, ECO:0000269|PubMed:23352267,
CC ECO:0000269|PubMed:24386374}.
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 -!- ACTIVITY REGULATION: Pyrrolopyrimidines inhibit both GyrB and its
CC paralog in topoisomerase IV (parE) (PubMed:23352267).
CC {ECO:0000269|PubMed:23352267, ECO:0000269|PubMed:24386374}.
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains.
CC Within the heterotetramer, GyrA contains the active site tyrosine that
CC forms a covalent intermediate with the DNA, while GyrB contributes the
CC cofactor binding sites and catalyzes ATP hydrolysis.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE016830; AAO79890.1; -; Genomic_DNA.
DR RefSeq; NP_813818.1; NC_004668.1.
DR PDB; 4GEE; X-ray; 1.70 A; A=18-224.
DR PDB; 4GFN; X-ray; 1.90 A; A=18-224.
DR PDB; 4GGL; X-ray; 1.69 A; A=18-224.
DR PDB; 4HXW; X-ray; 1.69 A; A=18-224.
DR PDB; 4K4O; X-ray; 1.30 A; A=18-224.
DR PDB; 4KSG; X-ray; 1.75 A; A=18-224.
DR PDB; 4KSH; X-ray; 1.70 A; A=18-224.
DR PDB; 4KTN; X-ray; 1.69 A; A=18-224.
DR PDBsum; 4GEE; -.
DR PDBsum; 4GFN; -.
DR PDBsum; 4GGL; -.
DR PDBsum; 4HXW; -.
DR PDBsum; 4K4O; -.
DR PDBsum; 4KSG; -.
DR PDBsum; 4KSH; -.
DR PDBsum; 4KTN; -.
DR AlphaFoldDB; Q839Z1; -.
DR SMR; Q839Z1; -.
DR STRING; 226185.EF_0005; -.
DR EnsemblBacteria; AAO79890; AAO79890; EF_0005.
DR KEGG; efa:EF0005; -.
DR PATRIC; fig|226185.9.peg.5; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_9; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000001415; Chromosome.
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 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 3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..642
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000435540"
FT DOMAIN 422..536
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 428
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 501
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 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 503
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 453
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 456
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT HELIX 19..24
FT /evidence="ECO:0007829|PDB:4K4O"
FT HELIX 26..30
FT /evidence="ECO:0007829|PDB:4K4O"
FT HELIX 35..54
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:4K4O"
FT TURN 86..88
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:4K4O"
FT HELIX 92..98
FT /evidence="ECO:0007829|PDB:4K4O"
FT HELIX 122..127
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 129..138
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 141..148
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 157..161
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 166..173
FT /evidence="ECO:0007829|PDB:4K4O"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:4K4O"
FT HELIX 186..199
FT /evidence="ECO:0007829|PDB:4K4O"
FT TURN 200..202
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 204..209
FT /evidence="ECO:0007829|PDB:4K4O"
FT STRAND 216..221
FT /evidence="ECO:0007829|PDB:4K4O"
SQ SEQUENCE 642 AA; 71878 MW; 7A5FD53203C6AEE0 CRC64;
MRERAQEYDA SQIQVLEGLE AVRKRPGMYI GSTSGEGLHH LVWEIVDNSI DEALAGFAKS
IQVIIEPDDS ITVIDDGRGI PVGIQAKTGR PAVETVFTVL HAGGKFGGGG YKVSGGLHGV
GSSVVNALST SLDVRVYKDG KVYYQEYRRG AVVDDLKVIE ETDRHGTTVH FIPDPEIFTE
TTVYDFDKLA TRVRELAFLN RGLHISIEDR REGQEDKKEY HYEGGIKSYV EHLNANKDVI
FPEPIFIEGE QQDITVEVSM QYTDGYHSNI LSFANNIHTY EGGTHESGFK TSLTRVINDY
ARKQKLMKEN DEKLTGEDVR EGLTAVVSIK HPDPQFEGQT KTKLGNSEVR TVTDRLFSEY
FTKFLMENPT VGKQIVEKGM LASKARLAAK RAREVTRRKG ALEISNLPGK LADCSSKDPE
KCELFIVEGD SAGGSAKQGR SREFQAILPI RGKILNVEKA SMDKILANEE IRSLFTAMGT
GFGEDFDVSK ARYHKLVIMT DADVDGAHIR TLLLTLFYRF MRPIVEAGYV YIAQPPLYGV
KQGKNITYVQ PGKHAEEELA KVLEELPASP KPSVQRYKGL GEMDDHQLWE TTMDPEKRLM
ARVSVDDAIE ADQIFEMLMG DRVEPRRAFI EENAHYVKNL DI
