ID F4GBU9_ALIDK Unreviewed; 860 AA.
AC F4GBU9;
DT 28-JUN-2011, integrated into UniProtKB/TrEMBL.
DT 28-JUN-2011, 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=Alide2_0003 {ECO:0000313|EMBL:AEB82443.1};
OS Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Alicycliphilus.
OX NCBI_TaxID=596154 {ECO:0000313|EMBL:AEB82443.1, ECO:0000313|Proteomes:UP000007938};
RN [1] {ECO:0000313|EMBL:AEB82443.1, ECO:0000313|Proteomes:UP000007938}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14773 / CIP 107495 / K601
RC {ECO:0000313|Proteomes:UP000007938};
RX PubMed=21742888; DOI=10.1128/JB.00365-11;
RA Oosterkamp M.J., Veuskens T., Plugge C.M., Langenhoff A.A., Gerritse J.,
RA van Berkel W.J., Pieper D.H., Junca H., Goodwin L.A., Daligault H.E.,
RA Bruce D.C., Detter J.C., Tapia R., Han C.S., Land M.L., Hauser L.J.,
RA Smidt H., Stams A.J.;
RT "Genome Sequences of Alicycliphilus denitrificans Strains BC and K601T.";
RL J. Bacteriol. 193:5028-5029(2011).
RN [2] {ECO:0000313|EMBL:AEB82443.1, ECO:0000313|Proteomes:UP000007938}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 14773 / CIP 107495 / K601
RC {ECO:0000313|Proteomes:UP000007938};
RG US DOE Joint Genome Institute;
RA Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA Peters L., Zeytun A., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA Kyrpides N., Ivanova N., Mikhailova N., Pagani I., Oosterkamp M.,
RA Pieper D., van Berkel W., Langenhoff A., Smidt H., Stams A., Woyke T.;
RT "Complete sequence of chromosome of Alicycliphilus denitrificans K601.";
RL Submitted (APR-2011) 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 ---------------------------------------------------------------------------
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; CP002657; AEB82443.1; -; Genomic_DNA.
DR RefSeq; WP_013721112.1; NC_015422.1.
DR AlphaFoldDB; F4GBU9; -.
DR STRING; 596154.Alide2_0003; -.
DR KEGG; adk:Alide2_0003; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_4; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000007938; 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; 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:UP000007938};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 461..587
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 467
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 552
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 552
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 554
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 492
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 495
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 860 AA; 94369 MW; AF7339ABACE8AF3D CRC64;
MTDENQPDPQ TTAPASVDAG GYGEGAIQIL EGLEAVRKRP GMYIGDTSDG TGLHHLVFEV
VDNSIDEALA GHCDDIVVTI HTDNSISVID NGRGIPTGVK MDDKHEPKRS AAEIALTELH
AGGKFNQNSY KVSGGLHGVG VSCVNALSKK LRLTVRRDGK THQLEFSKGV VQNRLIEVVD
GFEVSPMKIV GPTEKRGTEV RFLPDTEIFK ENSDFHYEIL AKRLRELSFL NNGVRIRLID
ERTGKEDDFS GAGGVKGFVE FINGTKKVLH PTAFHATGSR PAESYGGIPG TEIGVEVAMQ
WNDGYNEQVL CFTNNIPQRD GGTHLTGLRA AMTRVIGKYI EQNELAKKAK VDVSGDDMRE
GLCCVLSVKV PEPKFSSQTK DKLVSSEVRA PVEDIVAKAL TEYLEEKPQD AKILCGKIVE
AARAREAARK AREMTRRKGV LDGMGLPGKL ADCQEKDPAL CEIYIVEGDS AGGSAKQGRD
RKFQAILPLR GKILNVEKAR YEKLLSSNEI ITLITALGTG IGKASEDGNG KSGADDFDAA
KLRYHRIIIM TDADVDGAHI RTLLLTFFYR QMPELVERGH IYIAQPPLYK VKNGKEELYL
KDAAALDNFL LRVALNHASI STGGDAPRTL AGDELATLAR THQHAERVID RLSAFMDAEA
LRAAADGVAF NLDTLEDAQA SAVQLQARLR ELNTSGVPAD VTGEIDPRTD KPILRISRHH
HGNIKSSLIT QDFVAGDDYA ALAEAAESFR GLIQEGAKVM RGEGEKQKEE KISDFRQAMQ
WLIGEAERTT ARQRYKGLGE MNPEQLWETT MDPEVRRLLR VQIDDAIEAD RVFTMLMGDE
VEPRRDFIET NALRAGNIDV
//
