ID C7N0K4_SLAHD Unreviewed; 648 AA.
AC C7N0K4;
DT 13-OCT-2009, integrated into UniProtKB/TrEMBL.
DT 13-OCT-2009, sequence version 1.
DT 24-JAN-2024, entry version 95.
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=Shel_00050 {ECO:0000313|EMBL:ACV21082.1};
OS Slackia heliotrinireducens (strain ATCC 29202 / DSM 20476 / NCTC 11029 /
OS RHS 1) (Peptococcus heliotrinreducens).
OC Bacteria; Actinomycetota; Coriobacteriia; Eggerthellales; Eggerthellaceae;
OC Slackia.
OX NCBI_TaxID=471855 {ECO:0000313|EMBL:ACV21082.1, ECO:0000313|Proteomes:UP000002026};
RN [1] {ECO:0000313|EMBL:ACV21082.1, ECO:0000313|Proteomes:UP000002026}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29202 / DSM 20476 / NCTC 11029 / RHS 1
RC {ECO:0000313|Proteomes:UP000002026};
RX PubMed=21304663; DOI=10.4056/sigs.37633;
RA Pukall R., Lapidus A., Nolan M., Copeland A., Glavina Del Rio T., Lucas S.,
RA Chen F., Tice H., Cheng J.F., Chertkov O., Bruce D., Goodwin L., Kuske C.,
RA Brettin T., Detter J.C., Han C., Pitluck S., Pati A., Mavrommatis K.,
RA Ivanova N., Ovchinnikova G., Chen A., Palaniappan K., Schneider S.,
RA Rohde M., Chain P., D'haeseleer P., Goker M., Bristow J., Eisen J.A.,
RA Markowitz V., Kyrpides N.C., Klenk H.P., Hugenholtz P.;
RT "Complete genome sequence of Slackia heliotrinireducens type strain (RHS
RT 1).";
RL Stand. Genomic Sci. 1:234-241(2009).
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}.
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DR EMBL; CP001684; ACV21082.1; -; Genomic_DNA.
DR RefSeq; WP_012797193.1; NC_013165.1.
DR AlphaFoldDB; C7N0K4; -.
DR STRING; 471855.Shel_00050; -.
DR KEGG; shi:Shel_00050; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_1_2_11; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000002026; 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:0034335; F:DNA negative supercoiling activity; IEA:UniProt.
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; 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; 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}; 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:UP000002026};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 427..541
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 433
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 506
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 506
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 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 461
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 648 AA; 72027 MW; C722FD85102B0E12 CRC64;
MAEKQSSHYD AGDIQVLEGL EAVRKRPGMY IGSTGTRGLH HLVYEVVDNA VDEALAGYCT
KIDVIIHEDN SITVIDNGRG IPVEKHPKEK IPTVEVVLTI LHAGGKFGGE GYKVSGGLHG
VGVSCVNALS TRLEVEVCRD GKKYGIAFSR GKTVEKLHQI GTSKTTGTTV TFWPDPEIFT
DTLVYDYETL QERFREMAFL NKGLRIELTD ERQQDEEGNF KHETFKYDGG IVDFVKYLNQ
GKETLNKPIY FEAENADGTV EVVMQWSTSY GTNGIMAFAN NINTHEGGTH LDGFKNALTR
TINDYARSKG LLKEKDKNLT GDDAREGLAA IISVKLHDPQ FEGQTKTKLG NVEIRGLVQG
AVTKGLSEYL EENPTPAKRI VGKASQALKA REAARKAREM TRRKGVLDSF SMPGKLADCS
SREPALSEMF IVEGDSAGGS AKQARDRKYQ AILPLRGKIL NVERAGLHRA LSSDTISSLI
TAIGTNIGDD YNGDNARYHR IIIMTDADVD GAHIRCLLLT FFYRYMPDLI NRGYIYIAQP
PLYGLKKKNS ASGKILKYIY NDEAKDQIMA QLEDPDKYDI QRYKGLGEMD PEQLWETTME
PETRTLIQVS IEDAAAAERA VSDLMGDDVE PRKEFIQKNA LDVRFLDI
//