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Database: UniProt
Entry: A0A494XAS4_9BURK
LinkDB: A0A494XAS4_9BURK
Original site: A0A494XAS4_9BURK 
ID   A0A494XAS4_9BURK        Unreviewed;       823 AA.
AC   A0A494XAS4;
DT   05-JUN-2019, integrated into UniProtKB/TrEMBL.
DT   05-JUN-2019, sequence version 1.
DT   24-JAN-2024, entry version 19.
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   ECO:0000313|EMBL:RKP45556.1};
GN   ORFNames=D7S89_19625 {ECO:0000313|EMBL:RKP45556.1};
OS   Trinickia fusca.
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Trinickia.
OX   NCBI_TaxID=2419777 {ECO:0000313|EMBL:RKP45556.1, ECO:0000313|Proteomes:UP000280434};
RN   [1] {ECO:0000313|EMBL:RKP45556.1, ECO:0000313|Proteomes:UP000280434}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=7MK8-2 {ECO:0000313|EMBL:RKP45556.1,
RC   ECO:0000313|Proteomes:UP000280434};
RA   Gao Z.-H., Qiu L.-H.;
RT   "Paraburkholderia sp. 7MK8-2, isolated from soil.";
RL   Submitted (OCT-2018) 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. {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   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:RKP45556.1}.
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DR   EMBL; RBZV01000009; RKP45556.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A494XAS4; -.
DR   OrthoDB; 9802808at2; -.
DR   Proteomes; UP000280434; Unassembled WGS sequence.
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}; Reference proteome {ECO:0000313|Proteomes:UP000280434};
KW   Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW   Rule:MF_01898}.
FT   DOMAIN          441..556
FT                   /note="Toprim"
FT                   /evidence="ECO:0000259|PROSITE:PS50880"
FT   BINDING         447
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         521
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         521
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         523
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            472
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            475
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   823 AA;  91049 MW;  2CF4BA687CCFD346 CRC64;
     MSEQHNTQPD NSYGASSIQI LEGLEAVRKR PGMYIGDTSD GTGLHHLVFE VLDNSIDEAL
     AGHCNDIHVI IHADNSISVT DNGRGIPTDV KLDDKHDPKR SAAEIVMTEL HAGGKFDQNS
     YKVSGGLHGV GVSCVNALSS WLRLTVRRDG RKHFMEFHRG IAQNRVIEEV GGEQVSPMQY
     LGETENRGTE VHFLADETIF GKVEYHYDIL AKRIRELSFL NNGVRIRLTD QRSGKEDDFA
     FAGGVKGFVE YINKTKTVLH PTIFHIIGEK DGVGVEVSMQ WNDSYNENVL CFTNNIPQRD
     GGSHLTGLRA AMTRVINKYI ADHEIAKKAK VETSGDDMRE GLSCVLSVKV PEPKFSSQTK
     DKLVSSEVRA PVEEVVAKAL EEFLLETPND AKIICGKIID AARARDAARK AREMTRRKGV
     LDGVGLPGKL ADCQEKDPAK SEIYIVEGDS AGGSAKQGRD RKFQAILPLR GKVLNVEKAR
     YDKLLSSEQI VTLITALGCG IGKEDYNLDK LRYHRIIIMT DADVDGAHIR TLLLTFFYRQ
     MPEMIERGYI YIAQPPLYKV KAGKDERYLK DSAELNAHML RLALQGSELV PSEGATPIAG
     DALGELARSY LLAQGVVERL SRLYDANALE AVMDGVAIDL TSEASAQAAA QAIEAALRND
     PLKPEVSVYP MYDAVRELRS LRVERRHHGN VKVSVIDEEF LLTADYQQLL NTANTFKGLI
     GAGALIKRGE RSLAVADFKS AMRWLIADAE RNVSKQRYKG LGEMNPGQLW ETTMDPNVRR
     LLRVQIEDAI AADGIFTTLM GDEVEPRRAF IESNALRAGN IDV
//
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