ID GYRB_MYCTA Reviewed; 675 AA.
AC A5TY73; P41514; P77897;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 24-JAN-2024, entry version 95.
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=MRA_0005;
OS Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra).
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=419947;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7981652;
RA Madhusudan K., Ramesh V., Nagaraja V.;
RT "Molecular cloning of gyrA and gyrB genes of Mycobacterium tuberculosis:
RT analysis of nucleotide sequence.";
RL Biochem. Mol. Biol. Int. 33:651-660(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25177 / H37Ra;
RX PubMed=18584054; DOI=10.1371/journal.pone.0002375;
RA Zheng H., Lu L., Wang B., Pu S., Zhang X., Zhu G., Shi W., Zhang L.,
RA Wang H., Wang S., Zhao G., Zhang Y.;
RT "Genetic basis of virulence attenuation revealed by comparative genomic
RT analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv.";
RL PLoS ONE 3:E2375-E2375(2008).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABQ71723.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA55486.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X78888; CAA55486.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP000611; ABQ71723.1; ALT_INIT; Genomic_DNA.
DR PIR; S44198; S44198.
DR RefSeq; WP_003917863.1; NZ_CP016972.1.
DR AlphaFoldDB; A5TY73; -.
DR SMR; A5TY73; -.
DR GeneID; 45423962; -.
DR KEGG; mra:MRA_0005; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_11; -.
DR Proteomes; UP000001988; 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; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..675
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000300059"
FT DOMAIN 453..567
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 459
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 532
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 532
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 534
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 484
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 487
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 675 AA; 74091 MW; 4559D0D3FDAC8DC1 CRC64;
MAAQKKKAQD EYGAASITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV DNAVDEAMAG
YATTVNVVLL EDGGVEVADD GRGIPVATHA SGIPTVDVVM TQLHAGGKFD SDAYAISGGL
HGVGVSVVNA LSTRLEVEIK RDGYEWSQVY EKSEPLGLKQ GAPTKKTGST VRFWADPAVF
ETTEYDFETV ARRLQEMAFL NKGLTINLTD ERVTQDEVVD EVVSDVAEAP KSASERAAES
TAPHKVKSRT FHYPGGLVDF VKHINRTKNA IHSSIVDFSG KGTGHEVEIA MQWNAGYSES
VHTFANTINT HEGGTHEEGF RSALTSVVNK YAKDRKLLKD KDPNLTGDDI REGLAAVISV
KVSEPQFEGQ TKTKLGNTEV KSFVQKVCNE QLTHWFEANP TDAKVVVNKA VSSAQARIAA
RKARELVRRK SATDIGGLPG KLADCRSTDP RKSELYVVEG DSAGGSAKSG RDSMFQAILP
LRGKIINVEK ARIDRVLKNT EVQAIITALG TGIHDEFDIG KLRYHKIVLM ADADVDGQHI
STLLLTLLFR FMRPLIENGH VFLAQPPLYK LKWQRSDPEF AYSDRERDGL LEAGLKAGKK
INKEDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI LMGEDVDARR
SFITRNAKDV RFLDV
//
