ID E0UP19_SULAO Unreviewed; 772 AA.
AC E0UP19;
DT 02-NOV-2010, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2010, sequence version 1.
DT 27-MAR-2024, entry version 86.
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=Saut_0003 {ECO:0000313|EMBL:ADN08052.1};
OS Sulfurimonas autotrophica (strain ATCC BAA-671 / DSM 16294 / JCM 11897 /
OS OK10).
OC Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales;
OC Sulfurimonadaceae; Sulfurimonas.
OX NCBI_TaxID=563040 {ECO:0000313|EMBL:ADN08052.1, ECO:0000313|Proteomes:UP000007803};
RN [1] {ECO:0000313|EMBL:ADN08052.1, ECO:0000313|Proteomes:UP000007803}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-671 / DSM 16294 / JCM 11897 / OK10
RC {ECO:0000313|Proteomes:UP000007803};
RX PubMed=21304749;
RA Sikorski J., Munk C., Lapidus A., Ngatchou Djao O.D., Lucas S.,
RA Glavina Del Rio T., Nolan M., Tice H., Han C., Cheng J.F., Tapia R.,
RA Goodwin L., Pitluck S., Liolios K., Ivanova N., Mavromatis K.,
RA Mikhailova N., Pati A., Sims D., Meincke L., Brettin T., Detter J.C.,
RA Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J., Jeffries C.D.,
RA Rohde M., Lang E., Spring S., Goker M., Woyke T., Bristow J., Eisen J.A.,
RA Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Sulfurimonas autotrophica type strain
RT (OK10).";
RL Stand. Genomic Sci. 3:194-202(2010).
RN [2] {ECO:0000313|Proteomes:UP000007803}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-671 / DSM 16294 / JCM 11897 / OK10
RC {ECO:0000313|Proteomes:UP000007803};
RX DOI=10.4056/sigs.1173118;
RA Sikorski J., Munk C., Lapidus A., Djao O., Lucas S., Glavina Del Rio T.,
RA Nolan M., Tice H., Han C., Cheng J., Tapia R., Goodwin L., Pitluck S.,
RA Liolios K., Ivanova N., Mavromatis K., Mikhailova N., Pati A., Sims D.,
RA Meincke L., Brettin T., Detter J., Chen A., Palaniappan K., Land M.,
RA Hauser L., Chang Y., Jeffries C., Rohde M., Lang E., Spring S., Goker M.,
RA Woyke T., Bristow J., Eisen J., Markowitz V., Hugenholtz P., Kyrpides N.,
RA Klenk H.;
RT "Complete genome sequence of Sulfurimonas autotrophica type strain
RT (OK10T).";
RL Stand. Genomic Sci. 3:194-202(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;
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}.
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; CP002205; ADN08052.1; -; Genomic_DNA.
DR RefSeq; WP_013325808.1; NC_014506.1.
DR AlphaFoldDB; E0UP19; -.
DR STRING; 563040.Saut_0003; -.
DR KEGG; sua:Saut_0003; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_7; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000007803; 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; -; 2.
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; IPR049353; GyrB_hook.
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 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; PF21249; GyrB_hook; 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};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, 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:UP000007803};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 415..529
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 421
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 494
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 494
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 496
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 446
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 449
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 772 AA; 86949 MW; 48BAF049ED0653EC CRC64;
MQQEYGASNI KVLKGLEAVR KRPGMYIGDT GHRGLHHLVY EVIDNSIDEA MAGYCDTITV
TLTKNGTCKV SDNGRGIPTD MHPTENMSAA TVVLTVLHAG GKFDKDTYKV SGGLHGVGVS
VVNALSSDLH MTIYREGKIH EQDFKMGIPQ GPLEVTGTTR KTGTTIEFAA DPSIFTETIT
FEYEYLAKRF KELAYLNPFI TIKFNDERTN TKEVYHFEGG IAQYVSDMNK REVVANVYSF
SGKAEDIEFD IAIMYNDSYE EKLASFVNNI RTPNGGTHEA GFRAGLTRVI SNYNSKNGAA
KEKDVKISGD DVKEGLIAIV SARVPEPQFE GQTKGKLGNT YVRPLIQKAT GEALNKYFEE
NPIEAKAIVS KALMAARGRE AAKKARELTR RKDSMSVGTL PGKLADCQSK DASICELYLV
EGDSAGGSAK MGRDRVFQAI LPLKGKILNV EKARLEKILK SDEITNMITA MGCGIGEEYN
EEKLRYHKII IMTDADVDGS HIQTLLLTFF FRYFRDIIEK GYLYLAQPPL YRYKKGKKEI
YFKDDRAMND YLIDNGIESL DIDGVGHNDL VAYFKMVDHY ASSLEALNRR YALVKLIRHF
IENPDLIALP AKEMFVEIEK FLTSIGNNIL TYTINEETNE IHLFVQTQTG MEELLINDDL
FSAPHFNEAS FVYKKIMEWD IHFDKDIIEV LEDIKDYAKK GAYIQRYKGL GEMNPEQLWE
TTMTPENRVL LQISIEDAEV ASDAFTLFMG DEVEPRRNYI ETHAKDVKHL DV
//
