ID   D2RFU2_ARCPA            Unreviewed;       632 AA.
AC   D2RFU2;
DT   02-MAR-2010, integrated into UniProtKB/TrEMBL.
DT   02-MAR-2010, sequence version 1.
DT   27-MAR-2024, entry version 88.
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   OrderedLocusNames=Arcpr_0091 {ECO:0000313|EMBL:ADB57167.1};
OS   Archaeoglobus profundus (strain DSM 5631 / JCM 9629 / NBRC 100127 / Av18).
OC   Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC   Archaeoglobus.
OX   NCBI_TaxID=572546 {ECO:0000313|EMBL:ADB57167.1, ECO:0000313|Proteomes:UP000001901};
RN   [1] {ECO:0000313|EMBL:ADB57167.1, ECO:0000313|Proteomes:UP000001901}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 5631 / JCM 9629 / NBRC 100127 / Av18
RC   {ECO:0000313|Proteomes:UP000001901};
RX   PubMed=21304717;
RA   von Jan M., Lapidus A., Del Rio T.G., Copeland A., Tice H., Cheng J.F.,
RA   Lucas S., Chen F., Nolan M., Goodwin L., Han C., Pitluck S., Liolios K.,
RA   Ivanova N., Mavromatis K., Ovchinnikova G., Chertkov O., Pati A., Chen A.,
RA   Palaniappan K., Land M., Hauser L., Chang Y.J., Jeffries C.D., Saunders E.,
RA   Brettin T., Detter J.C., Chain P., Eichinger K., Huber H., Spring S.,
RA   Rohde M., Goker M., Wirth R., Woyke T., Bristow J., Eisen J.A.,
RA   Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT   "Complete genome sequence of Archaeoglobus profundus type strain (AV18).";
RL   Stand. Genomic Sci. 2:327-346(2010).
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; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_01898};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_01898};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000256|HAMAP-
CC         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; CP001857; ADB57167.1; -; Genomic_DNA.
DR   AlphaFoldDB; D2RFU2; -.
DR   STRING; 572546.Arcpr_0091; -.
DR   PaxDb; 572546-Arcpr_0091; -.
DR   KEGG; apo:Arcpr_0091; -.
DR   eggNOG; arCOG04371; Archaea.
DR   HOGENOM; CLU_006146_4_1_2; -.
DR   Proteomes; UP000001901; 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; cd16928; HATPase_GyrB-like; 1.
DR   CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR   CDD; cd03366; TOPRIM_TopoIIA_GyrB; 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; IPR006171; TOPRIM_domain.
DR   InterPro; IPR034160; TOPRIM_GyrB.
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; 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:UP000001901};
KW   Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW   Rule:MF_01898}.
FT   DOMAIN          419..533
FT                   /note="Toprim"
FT                   /evidence="ECO:0000259|PROSITE:PS50880"
FT   BINDING         425
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         498
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         498
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         500
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            450
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            453
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   632 AA;  71239 MW;  FE241AE80D8F7551 CRC64;
     MPISSTFLAM SDYTAEAIEV LDDIQAVRKR PGMYVGSTGS RGFHHLLWEI VDNSIDEALA
     GYCNRIVVTL HKDGSASVED NGRGIPVEEH PIFKKPALEI VMTKLHAGGK FSKKAYKVSG
     GLHGVGLSVV NALSEWLEVW VKRNGKIYYQ RYERGKPVTP LKVVGETKET GTKIRFKPDP
     EIFEVKEFDY DVVAERLREL AFLNKGLRIK LIDERTGKVK EFYSEEGIVG FVKYLNKGKD
     VITDVVYISG EKNGINVEIA FQFTNEDFEN LLAFANNIHT IEGGTHVSGF RAGLTRAINE
     YGKKHVKKFT PISGSDIREG LTAVLSVKVP EPQFEGQTKT KLTNSDVKTV VESLVYNNFL
     RWLEEHPSEA QRIIEKCLLA MKAREMARRA RELVKRKAEI SLTLPGKLAD CSSKNVEERE
     LFIVEGESAG GSAKQARDRR FQAVLPIRGK IINVEKAGML RALKNEEIKA IASAIGGGIG
     KDFDLSKVRY GKIIIMTDAD VDGAHIRTLL LTFFYRYMRP LIEAGMVYIA LPPLYRVKKG
     DKVYYVYSEK ELRDVLKKIG KAEVQRFKGL GEMNPEQLWE TAMNPKTRKL VKVTIEDALI
     AEKMFRILMG ENVDERKEFI LNHAKEVKNL DV
//