GYRB_METH1
ID GYRB_METH1 Reviewed; 648 AA.
AC P43053; D1J8G4;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 02-MAR-2010, sequence version 2.
DT 03-AUG-2022, entry version 119.
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=MHO_3760;
OS Metamycoplasma hominis (strain ATCC 23114 / DSM 25592 / NBRC 14850 / NCTC
OS 10111 / PG21) (Mycoplasma hominis).
OC Bacteria; Tenericutes; Mycoplasmoidales; Metamycoplasmataceae;
OC Metamycoplasma.
OX NCBI_TaxID=347256;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7521872; DOI=10.1128/jb.176.18.5835-5842.1994;
RA Ladefoged S.A., Christiansen G.;
RT "Sequencing analysis reveals a unique gene organization in the gyrB region
RT of Mycoplasma hominis.";
RL J. Bacteriol. 176:5835-5842(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 23114 / DSM 25592 / NBRC 14850 / NCTC 10111 / PG21;
RX PubMed=19816563; DOI=10.1371/journal.pgen.1000677;
RA Pereyre S., Sirand-Pugnet P., Beven L., Charron A., Renaudin H., Barre A.,
RA Avenaud P., Jacob D., Couloux A., Barbe V., de Daruvar A., Blanchard A.,
RA Bebear C.;
RT "Life on arginine for Mycoplasma hominis: clues from its minimal genome and
RT comparison with other human urogenital mycoplasmas.";
RL PLoS Genet. 5:E1000677-E1000677(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: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 -!- 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; X77529; CAA54665.1; -; Genomic_DNA.
DR EMBL; FP236530; CAX37511.1; -; Genomic_DNA.
DR RefSeq; WP_012855650.1; NC_013511.1.
DR AlphaFoldDB; P43053; -.
DR SMR; P43053; -.
DR STRING; 347256.MHO_3760; -.
DR EnsemblBacteria; CAX37511; CAX37511; MHO_3760.
DR KEGG; mho:MHO_3760; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_14; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000002631; 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 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 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 PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..648
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145320"
FT DOMAIN 432..546
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 438
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 511
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 511
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 513
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 463
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 165
FT /note="V -> F (in Ref. 1; CAA54665)"
FT /evidence="ECO:0000305"
FT CONFLICT 189
FT /note="D -> F (in Ref. 1; CAA54665)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 648 AA; 72640 MW; D8CE9E4ED8B4FCCB CRC64;
MDKIEEIHKY NADNIQILEG LEAVRKRPGM YIGSIGFKGL HHLLWEIVDN SVDEAMAGFA
TEIKIKLYPN NVIEVEDNGR GMPTGIHSGT KKSAVETILT VLHAGGKFDG SNYKVSGGLH
GVGASVVNAL SSEFEVWVKR DGKLHYQQFR NGGIPVKPLE VIGNVSEVET GTTIKFHPDY
TIMEKENFDF DTIIDHSKQI AYLNKGLKIT VENVEKNIIK VFCFEGGLID YVKELNKGKK
LIVPEVIYAE GVFNDKNFTN GQDVIVEVAM QYNEAYTNSI VSYANNIQTI DGGTHEQGFY
DALVRIYNNY AETNKLFKTS SEKITREDVK EGLVAIISIK HTDPIFEGQT KGKLENKDAR
IATNKILSDS LERYLNENPE IARAIIEKCL LSQHTRLLEI KAREASRKGN GLDLGNLPGK
LADCSSKNAE IRELFIVEGN SAGGSAKMGR DRSIQAILPL RGKVINAEKN SFASVLSNKE
IATMIHALGT GINTEFDINK LKYHKIIIMT DADVDGAHIT TLLLTFFYRY MKPLIEYGFV
YLAQPPLYKI TSGKNVEYAY NDLQKEQIMA KLEDKRNVAI QRYKGLGEMD PEQLWETTMD
PETRKMLQVQ IDDAAICDTV FATLMGEEIE PRHDFIQENA KYANNIDI
