GYRB_THET8
ID GYRB_THET8 Reviewed; 634 AA.
AC Q5SHZ4; Q9LCX5;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 130.
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=TTHA1586;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Hoermann L., Bronner C., Forster A., Mousli M., Lutz Y., Oudet P.,
RA Jeltsch J.M.;
RT "The Thermus thermophilus gyrase: cloning, expression and activity of the
RT gyrase A and gyrase B subunits.";
RL Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-390 IN COMPLEX WITH NOVOBIOCIN,
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND DOMAIN.
RX PubMed=11850422; DOI=10.1074/jbc.m111740200;
RA Lamour V., Hoermann L., Jeltsch J.M., Oudet P., Moras D.;
RT "An open conformation of the Thermus thermophilus gyrase B ATP-binding
RT domain.";
RL J. Biol. Chem. 277:18947-18953(2002).
RN [4]
RP FUNCTION, STRUCTURE BY ELECTRON MICROSCOPY (16.8 ANGSTROMS), STRUCTURE BY
RP ELECTRON MICROSCOPY (23 ANGSTROMS) IN COMPLEX WITH DNA AND CIPROFOXACIN,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, DOMAIN, AND DNA-BINDING.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=23804759; DOI=10.1093/nar/gkt560;
RA Papillon J., Menetret J.F., Batisse C., Helye R., Schultz P., Potier N.,
RA Lamour V.;
RT "Structural insight into negative DNA supercoiling by DNA gyrase, a
RT bacterial type 2A DNA topoisomerase.";
RL Nucleic Acids Res. 41:7815-7827(2013).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner
CC (PubMed:23804759, PubMed:11850422). It probably also catalyzes the
CC interconversion of other topological isomers of double-stranded DNA
CC rings, including catenanes (PubMed:11850422). Relaxes negatively
CC supercoiled DNA in an ATP-independent manner (PubMed:23804759,
CC PubMed:11850422). At comparable concentrations T.thermophilus gyrase
CC does not introduce as many negative supercoils into DNA as the E.coli
CC enzyme (PubMed:23804759). {ECO:0000269|PubMed:23804759}.
CC -!- FUNCTION: Negative supercoiling favors strand separation, and DNA
CC replication, transcription, recombination and repair, all of which
CC involve strand separation. Type II topoisomerases break and join 2 DNA
CC strands simultaneously in an ATP-dependent manner.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 65 degrees Celsius (PubMed:23804759,
CC PubMed:11850422). Active between 25 and 77 degrees Celsius
CC (PubMed:11850422). {ECO:0000269|PubMed:11850422,
CC ECO:0000269|PubMed:23804759};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC (PubMed:23804759). Non-hydrolyzable ATP analogs induce dimerization,
CC novobiocin also induces a small amount of dimerization
CC (PubMed:11850422). The two subunits form an intertwined dimer where the
CC GyrB ATPase transducer helix of 1 subunit connects to the Toprim domain
CC of the other GyrB subunit through a 10 residue linker
CC (PubMed:23804759). In the heterotetramer, GyrA contains the active site
CC tyrosine that forms a covalent intermediate with the DNA, while GyrB
CC binds cofactors and catalyzes ATP hydrolysis.
CC {ECO:0000269|PubMed:11850422, ECO:0000305|PubMed:23804759}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- DOMAIN: Consists of 3 domains; the ATPase domain (residues 1-220), the
CC transducer domain (221-390) and the toprim domain (391-634)
CC (PubMed:11850422). Removal of the N-terminal ATPase domain (residues 2-
CC 392) increases ATP-independent DNA relaxation, showing it is not
CC required for DNA binding or cleavage, this enzyme still has some
CC supercoiling activity, but in this case it introduces positive
CC supercoils (PubMed:23804759). {ECO:0000269|PubMed:23804759,
CC ECO:0000305|PubMed:11850422}.
CC -!- MISCELLANEOUS: For the electron microscopy studies a GyrB-GyrA fusion
CC protein was made with a Gly-Asp-Leu linker between the 2 subunits. It
CC forms the expected dimer (PubMed:23804759).
CC {ECO:0000269|PubMed:23804759}.
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; AF167433; AAF89615.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD71409.1; -; Genomic_DNA.
DR RefSeq; WP_011228788.1; NC_006461.1.
DR RefSeq; YP_144852.1; NC_006461.1.
DR PDB; 1KIJ; X-ray; 2.30 A; A/B=1-390.
DR PDB; 6ENH; X-ray; 1.94 A; A=1-390.
DR PDBsum; 1KIJ; -.
DR PDBsum; 6ENH; -.
DR AlphaFoldDB; Q5SHZ4; -.
DR SMR; Q5SHZ4; -.
DR STRING; 300852.55772968; -.
DR DrugBank; DB01942; Formic acid.
DR PRIDE; Q5SHZ4; -.
DR EnsemblBacteria; BAD71409; BAD71409; BAD71409.
DR GeneID; 3170041; -.
DR KEGG; ttj:TTHA1586; -.
DR PATRIC; fig|300852.9.peg.1556; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_0; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; Q5SHZ4; -.
DR Proteomes; UP000000532; 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:0034335; F:DNA negative supercoiling activity; IDA:UniProtKB.
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..634
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000435543"
FT DOMAIN 416..534
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 1..220
FT /note="ATPase domain"
FT /evidence="ECO:0000305|PubMed:11850422"
FT REGION 221..390
FT /note="Transducer domain"
FT /evidence="ECO:0000305|PubMed:11850422"
FT BINDING 422
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 499
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 499
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
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 SITE 447
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 450
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 93
FT /note="T -> N (in Ref. 1; AAF89615)"
FT /evidence="ECO:0000305"
FT CONFLICT 475..476
FT /note="GI -> AV (in Ref. 1; AAF89615)"
FT /evidence="ECO:0000305"
FT HELIX 8..11
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 14..19
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 22..25
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 30..49
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 66..73
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:6ENH"
FT TURN 81..84
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 87..93
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:1KIJ"
FT HELIX 100..103
FT /evidence="ECO:0007829|PDB:1KIJ"
FT HELIX 115..122
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 124..133
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 136..143
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 146..156
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:1KIJ"
FT STRAND 163..170
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 172..175
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 182..195
FT /evidence="ECO:0007829|PDB:6ENH"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:1KIJ"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:6ENH"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 211..214
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 219..227
FT /evidence="ECO:0007829|PDB:6ENH"
FT TURN 228..230
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 239..245
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 248..260
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 263..268
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 278..297
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 303..305
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 311..314
FT /evidence="ECO:0007829|PDB:6ENH"
FT STRAND 317..324
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 341..361
FT /evidence="ECO:0007829|PDB:6ENH"
FT HELIX 363..389
FT /evidence="ECO:0007829|PDB:6ENH"
SQ SEQUENCE 634 AA; 70524 MW; 1276B82F82DAC561 CRC64;
MSYDASAIRV LKGLEGVRHR PAMYIGGTGV EGYHHLFKEI LDNAVDEALA GYATEILVRL
NEDGSLTVED NGRGIPVDLM PEEGKPAVEV IYTTLHSGGK FEQGAYKVSG GLHGVGASVV
NALSEWTVVE VFREGKHHRI AFSRGEVTEP LRVVGEAPRG KTGTRVTFKP DPEIFGNLRF
DPSKIRARLR EVAYLVAGLK LVFQDRQHGK EEVFLDKGGV ASFAKALAEG EDLLYEKPFL
IRGTHGEVEV EVGFLHTQGY NAEILTYANM IPTRDGGTHL TAFKSAYSRA LNQYAKKAGL
NKEKGPQPTG DDLLEGLYAV VSVKLPNPQF EGQTKGKLLN PEAGTAVGQV VYERLLEILE
ENPRIAKAVY EKALRAAQAR EAARKARELV RRQNPLESDE LPGKLADCQT ENPEEAELFI
VEGDSAGGSA KQGRDRRFQA ILPLRGKILN VEKAGLSKAL KNAEVRAMVS AIGVGIGGDG
EAHFDLEGLR YHKIIIMTDA DVDGSHIRTL LLTFFYRYMR PLIERGHVYI AQPPLYRLQV
GKKVEYLYSD EELQARLKEL EGKHYEVQRF KGLGEMNPEQ LWETTMNPEK RVLKRVELQD
ALEASELFEK LMGQEVAPRR EFIEEHARYA ELDI
