ID N8SHF2_9GAMM Unreviewed; 822 AA.
AC N8SHF2;
DT 26-JUN-2013, integrated into UniProtKB/TrEMBL.
DT 26-JUN-2013, sequence version 1.
DT 24-JAN-2024, entry version 69.
DE RecName: Full=DNA gyrase subunit B {ECO:0000256|ARBA:ARBA00019166, ECO:0000256|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000256|ARBA:ARBA00012895, ECO:0000256|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN ECO:0000313|EMBL:PJF05647.1};
GN ORFNames=CVD06_00640 {ECO:0000313|EMBL:PJF05647.1}, E2R16_18210
GN {ECO:0000313|EMBL:TEU25203.1}, F985_00004
GN {ECO:0000313|EMBL:ENU45289.1}, IC763_00020
GN {ECO:0000313|EMBL:QNY27533.1}, IC769_00020
GN {ECO:0000313|EMBL:QNY06452.1}, IC776_00020
GN {ECO:0000313|EMBL:QNX72350.1}, IC796_00020
GN {ECO:0000313|EMBL:QNX05417.1};
OS Acinetobacter seifertii.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Moraxellales; Moraxellaceae;
OC Acinetobacter; Acinetobacter calcoaceticus/baumannii complex.
OX NCBI_TaxID=1530123 {ECO:0000313|EMBL:ENU45289.1, ECO:0000313|Proteomes:UP000013065};
RN [1] {ECO:0000313|Proteomes:UP000013065}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NIPH 973 {ECO:0000313|Proteomes:UP000013065};
RG The Broad Institute Genome Sequencing Platform;
RG The Broad Institute Genome Sequencing Center for Infectious Disease;
RA Cerqueira G., Feldgarden M., Courvalin P., Perichon B.,
RA Grillot-Courvalin C., Clermont D., Rocha E., Yoon E.-J., Nemec A.,
RA Walker B., Young S.K., Zeng Q., Gargeya S., Fitzgerald M., Haas B.,
RA Abouelleil A., Alvarado L., Arachchi H.M., Berlin A.M., Chapman S.B.,
RA Dewar J., Goldberg J., Griggs A., Gujja S., Hansen M., Howarth C.,
RA Imamovic A., Larimer J., McCowan C., Murphy C., Neiman D., Pearson M.,
RA Priest M., Roberts A., Saif S., Shea T., Sisk P., Sykes S., Wortman J.,
RA Nusbaum C., Birren B.;
RT "The Genome Sequence of Acinetobacter sp. NIPH 973.";
RL Submitted (FEB-2013) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ENU45289.1, ECO:0000313|Proteomes:UP000013065}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NIPH 973 {ECO:0000313|EMBL:ENU45289.1,
RC ECO:0000313|Proteomes:UP000013065};
RX PubMed=25563912; DOI=10.1099/ijs.0.000043;
RA Nemec A., Krizova L., Maixnerova M., Sedo O., Brisse S., Higgins P.G.;
RT "Acinetobacter seifertii sp. nov., a member of the Acinetobacter
RT calcoaceticus-Acinetobacter baumannii complex isolated from human clinical
RT specimens.";
RL Int. J. Syst. Evol. Microbiol. 65:934-942(2015).
RN [3] {ECO:0000313|EMBL:PJF05647.1, ECO:0000313|Proteomes:UP000229898}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MI30-324 {ECO:0000313|EMBL:PJF05647.1,
RC ECO:0000313|Proteomes:UP000229898};
RA Cerezales M., Xanthopoulou K., Ertel J., Nemec A., Bustamante Z.,
RA Seifert H., Gallego L., Higgins P.G.;
RT "Acinetobacter seifertii isolated from Bolivian hospitals; a case of
RT mistaken identity.";
RL Submitted (NOV-2017) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:TEU25203.1, ECO:0000313|Proteomes:UP000297445}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SAb133 {ECO:0000313|EMBL:TEU25203.1,
RC ECO:0000313|Proteomes:UP000297445};
RA Furlan J.P.R., Stehling E.G.;
RT "Draft genome sequence of an environmental Acinetobacter seifertii from
RT Brazil.";
RL Submitted (MAR-2019) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000313|Proteomes:UP000516666, ECO:0000313|Proteomes:UP000516799}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AS23 {ECO:0000313|EMBL:QNY06452.1}, AS39
RC {ECO:0000313|Proteomes:UP000516666}, AS4 {ECO:0000313|EMBL:QNY27533.1,
RC ECO:0000313|Proteomes:UP000516799}, and AS73
RC {ECO:0000313|EMBL:QNX05417.1, ECO:0000313|Proteomes:UP000516862};
RA Li L.-H., Yang Y.-S., Sun J.-R., Huang T.-W., Huang W.-C., Wang Y.-C.,
RA Kuo T.-H., Kuo S.-C., Chen T.-L.;
RT "Clinical and molecular characterization of Acinetobacter seifertii in
RT Taiwan.";
RL Submitted (SEP-2020) to the EMBL/GenBank/DDBJ databases.
RN [6] {ECO:0000313|Proteomes:UP000516666, ECO:0000313|Proteomes:UP000516688}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AS23 {ECO:0000313|EMBL:QNY06452.1,
RC ECO:0000313|Proteomes:UP000516688}, AS39 {ECO:0000313|EMBL:QNX72350.1,
RC ECO:0000313|Proteomes:UP000516666}, AS4 {ECO:0000313|EMBL:QNY27533.1,
RC ECO:0000313|Proteomes:UP000516799}, and AS73
RC {ECO:0000313|EMBL:QNX05417.1, ECO:0000313|Proteomes:UP000516862};
RA Chen F.-J., Lee Y.-T.;
RL Submitted (SEP-2020) to the EMBL/GenBank/DDBJ databases.
RN [7] {ECO:0000313|EMBL:QNX72350.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=AS23 {ECO:0000313|Proteomes:UP000516688}, and AS39
RC {ECO:0000313|EMBL:QNX72350.1};
RA Li L.-H., Yang Y.-S., Sun J.-R., Huang T.-W., Huang W.-C., Wang Y.-C.,
RA Kuo T.-H., Kuo S.-C., Chen T.-L.;
RT "Clinical and molecular characterization of Acinetobacter seifertii in
RT Taiwan.";
RL Submitted (MAR-2021) to the EMBL/GenBank/DDBJ databases.
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.
CC {ECO:0000256|ARBA:ARBA00001978, ECO:0000256|HAMAP-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|ARBA:ARBA00011234,
CC ECO:0000256|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|ARBA:ARBA00004496,
CC 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; APOO01000001; ENU45289.1; -; Genomic_DNA.
DR EMBL; PGPD01000007; PJF05647.1; -; Genomic_DNA.
DR EMBL; CP061561; QNX05417.1; -; Genomic_DNA.
DR EMBL; CP061646; QNX72350.1; -; Genomic_DNA.
DR EMBL; CP061672; QNY06452.1; -; Genomic_DNA.
DR EMBL; CP061687; QNY27533.1; -; Genomic_DNA.
DR EMBL; SNSA01000013; TEU25203.1; -; Genomic_DNA.
DR RefSeq; WP_004698165.1; NZ_SNSA01000013.1.
DR GeneID; 60734248; -.
DR PATRIC; fig|520709.3.peg.4; -.
DR HOGENOM; CLU_006146_4_1_6; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000013065; Unassembled WGS sequence.
DR Proteomes; UP000229898; Unassembled WGS sequence.
DR Proteomes; UP000297445; Unassembled WGS sequence.
DR Proteomes; UP000516666; Chromosome.
DR Proteomes; UP000516688; Chromosome.
DR Proteomes; UP000516799; Chromosome.
DR Proteomes; UP000516862; 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; 3.10.20.690; -; 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; IPR041423; GyrB_insert.
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; PF18053; GyrB_insert; 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};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 431..546
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 437
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 511
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 511
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 513
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 462
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 465
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 822 AA; 92165 MW; 42D13C5AC801290E CRC64;
MSSESQSASQ TEQTNEKAYD SSSIKVLRGL DAVRKRPGMY IGDTDDGTGL HHMVFEVVDN
AIDEALAGHC DEIIVTIHED ESVSVSDNGR GIPTDIHPEE GVSAAEVILT ILHAGGKFDD
NSYKVSGGLH GVGVSVVNAL SSKLHLIINR AGQVHEQEYQ HGDPQYPLRV IGETDSSGTT
VRFWPSELTF SQTIFNVEIL ARRLRELSFL NAGVRIVLRD ERINLEHVYD YEGGLSEFVK
YINEGKTHLN EIFHFTADTE SGIGVEVALQ WNESYQENVR CFTNNIPQKD GGTHLAGFRA
ALTRGLNQYL ENENILKKEK VNVTGDDARE GLTAIISVKV PDPKFSSQTK EKLVSSEVKP
AVEQAMNKEF SAYLLENPQA AKSIAGKIID AARARDAARK AREMTRRKSA LDIAGLPGKL
ADCQEKDPAL SELYLVEGDS AGGSAKQGRN RKMQAILPLK GKILNVERAR FDKMISSQEV
GTLITALGCG IGREEYNPDK LRYHKIIIMT DADVDGSHIR TLLLTFFFRQ MPELVERGHI
YIAQPPLYKL KKGKQEQYIK DNDALETYLI SNAIDELALH ISAEAPAITG EALAKVIQDY
QVSQKSLQRL TLRYPASLLD ALLEMEAFKA DQNHDQAYVQ QWADQVREAI QRLQPSLRPE
ITLETFEREN AQGEKTAHYW PRVTVYVHNL PHAYLLDAGL LNSAEYARLL KNSKSWFKLI
EDGAYLQKGD RRIQVANFHQ VWQHILQDSR RGMMIQRYKG LGEMNAEQLW ETTMDPENRN
MLQVTIDDAI EADRMFSCLM GDDVEPRRAF IEENALNADI DA
//
