GYRB_TREPA
ID GYRB_TREPA Reviewed; 637 AA.
AC O08399;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=TP_1006;
OS Treponema pallidum (strain Nichols).
OC Bacteria; Spirochaetes; Spirochaetales; Treponemataceae; Treponema.
OX NCBI_TaxID=243276;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Nichols;
RX PubMed=9252582; DOI=10.1111/j.1574-6968.1997.tb10473.x;
RA Stamm L.V., Greene S.R., Barnes N.Y.;
RT "Identification and characterization of the gyrB gene from Treponema
RT pallidum subsp. pallidum.";
RL FEMS Microbiol. Lett. 153:129-134(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nichols;
RX PubMed=9665876; DOI=10.1126/science.281.5375.375;
RA Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Clayton R.A., Ketchum K.A.,
RA Sodergren E., Hardham J.M., McLeod M.P., Salzberg S.L., Peterson J.D.,
RA Khalak H.G., Richardson D.L., Howell J.K., Chidambaram M., Utterback T.R.,
RA McDonald L.A., Artiach P., Bowman C., Cotton M.D., Fujii C., Garland S.A.,
RA Hatch B., Horst K., Roberts K.M., Sandusky M., Weidman J.F., Smith H.O.,
RA Venter J.C.;
RT "Complete genome sequence of Treponema pallidum, the syphilis spirochete.";
RL Science 281:375-388(1998).
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:0000255|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:0000255|HAMAP-
CC Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_01898}.
CC -!- INTERACTION:
CC O08399; O83050: TP_0004; NbExp=2; IntAct=EBI-1585657, EBI-1584836;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|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:0000255|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; U78094; AAB66715.1; -; Genomic_DNA.
DR EMBL; AE000520; AAC65954.1; -; Genomic_DNA.
DR PIR; H71254; H71254.
DR RefSeq; WP_010882450.1; NC_021490.2.
DR AlphaFoldDB; O08399; -.
DR SMR; O08399; -.
DR IntAct; O08399; 3.
DR STRING; 243276.TPANIC_1006; -.
DR EnsemblBacteria; AAC65954; AAC65954; TP_1006.
DR GeneID; 57879517; -.
DR KEGG; tpa:TP_1006; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_1_2_12; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000000811; 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; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 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_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
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 Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..637
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145357"
FT DOMAIN 422..536
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 428
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 503
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 453
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 456
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 637 AA; 70910 MW; 8131F25CFCDB91E4 CRC64;
MGIEYSASSI TVLEGLEAVR KRPGMYIGST GPNGLHHLVY EVVDNCIDEA MAGYCDRITV
VLEQGNVVRV EDNGRGIPVD VHPHEGVSAL EVVLTKLHAG GKFDKKSYKV SGGLHGVGVS
VVNALSLWVE VTVYRDGAEY YQKFNVGMPL APVEKRGVSE KRGTIIRWQA DPSIFKETVA
YDFDVLLTRL RELAFLNSTV VIQLRDERLA TAKQVEFAFE GGIRHFVSYL NRGKSVVPER
PLYIEGSKSD VLVEVALQYH DGYTENVQSF VNDINTREGG THLEGFKSAL TRVANDFLKK
SPKLAKKIER EEKLVGEDVR AGLTVVLSVK IPEPQFEGQT KTKLGNSEVR GIVDSLVGER
LTLYFEQNPG VLTKILEKSI AEAQARLAAR RAKEAARRKS GMDSFGLPGK LADCSLKDPA
KCEVYIVEGD SAGGSAKKGR DSKTQAILPL WGKMLNVEKT RLDKVLHNEK LQPIIATLGT
GVGKDFDLTR IRYHKVIIMA DADVDGSHIR TLLLTFFFRY LPQIIEAGYV YLAMPPLYRI
AWSKKELYVY SDTERDEALE SIGKKSGVAV QRYKGLGEMD GTQLWETTMN PVRRKMMQVV
LSDAVEADRV FSTLMGEDVE PRRKFIEENA IYARLDV
