ID   GYRB_MYCSM              Reviewed;         675 AA.
AC   P0C559; P48355; Q59555;
DT   10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT   10-JUL-2007, sequence version 1.
DT   27-MAR-2024, entry version 83.
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, ECO:0000269|PubMed:12000834};
GN   Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898};
OS   Mycolicibacterium smegmatis (Mycobacterium smegmatis).
OC   Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC   Mycolicibacterium.
OX   NCBI_TaxID=1772;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, ACTIVITY REGULATION, AND
RP   SUBUNIT.
RC   STRAIN=ATCC 27204 / DSM 43464 / SN2;
RX   PubMed=8574396; DOI=10.1099/13500872-141-12-3029;
RA   Madhusudan K., Nagaraja V.;
RT   "Mycobacterium smegmatis DNA gyrase: cloning and overexpression in
RT   Escherichia coli.";
RL   Microbiology 141:3029-3037(1995).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692;
RX   PubMed=8733228; DOI=10.1111/j.1365-2958.1996.tb02617.x;
RA   Salazar L., Fsihi H., De Rossi E., Riccardi G., Rios C., Cole S.T.,
RA   Takiff H.E.;
RT   "Organization of the origins of replication of the chromosomes of
RT   Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium
RT   tuberculosis and isolation of a functional origin from M. smegmatis.";
RL   Mol. Microbiol. 20:283-293(1996).
RN   [3]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, SUBUNIT,
RP   SUBCELLULAR LOCATION, AND DNA-BINDING.
RC   STRAIN=ATCC 27204 / DSM 43464 / SN2;
RX   PubMed=12000834; DOI=10.1093/nar/30.10.2144;
RA   Manjunatha U.H., Dalal M., Chatterji M., Radha D.R., Visweswariah S.S.,
RA   Nagaraja V.;
RT   "Functional characterisation of mycobacterial DNA gyrase: an efficient
RT   decatenase.";
RL   Nucleic Acids Res. 30:2144-2153(2002).
CC   -!- FUNCTION: Supercoils relaxed DNA in an ATP-dependent manner
CC       (PubMed:8574396). A type II topoisomerase that negatively supercoils
CC       closed circular double-stranded (ds) DNA in an ATP-dependent manner to
CC       modulate DNA topology and maintain chromosomes in an underwound state,
CC       also catalyzes the interconversion of other topological isomers of
CC       double-stranded DNA rings, including catenanes (PubMed:12000834). At
CC       comparable concentrations has a stronger decatenation activity than
CC       E.coli, which is inhibited by ciprofloxacin and novobiocin
CC       (PubMed:12000834). Cleaves dsDNA at the sequence 5'-AT/GGCC-3', leaving
CC       a 4 base overhang (PubMed:12000834). Relaxes negatively supercoiled DNA
CC       in an ATP-independent manner (PubMed:12000834).
CC       {ECO:0000269|PubMed:12000834, ECO:0000269|PubMed:8574396}.
CC   -!- FUNCTION: Negative supercoiling favors strand separation, and DNA
CC       replication, transcription, recombination and repair, all of which
CC       involve strand separation. Type II topoisomerases break and join 2 DNA
CC       strands simultaneously in an ATP-dependent manner.
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-Rule:MF_01898,
CC         ECO:0000269|PubMed:12000834};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01898, ECO:0000269|PubMed:12000834};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01898};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000255|HAMAP-
CC         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   -!- ACTIVITY REGULATION: DNA supercoiling is inhibited by the coumarin
CC       antibiotic novobiocin (PubMed:8574396). Also inhibited by the
CC       fluoroquinolones ciprofloxacin and moxifloxacin (PubMed:12000834).
CC       {ECO:0000269|PubMed:12000834, ECO:0000269|PubMed:8574396}.
CC   -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC       (PubMed:12000834, PubMed:8574396). In the heterotetramer, GyrA contains
CC       the active site tyrosine that forms a transient covalent intermediate
CC       with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.
CC       {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:12000834,
CC       ECO:0000305|PubMed:8574396}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898,
CC       ECO:0000269|PubMed:12000834}.
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=CAA63253.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; X92503; CAA63253.1; ALT_INIT; Genomic_DNA.
DR   EMBL; X84077; CAA58884.1; -; Genomic_DNA.
DR   RefSeq; WP_003891333.1; NZ_UGQO01000001.1.
DR   PDB; 4BAE; X-ray; 2.35 A; A/B/C/D=19-212.
DR   PDB; 6Y8O; X-ray; 1.60 A; A/B=9-218.
DR   PDBsum; 4BAE; -.
DR   PDBsum; 6Y8O; -.
DR   AlphaFoldDB; P0C559; -.
DR   SMR; P0C559; -.
DR   BindingDB; P0C559; -.
DR   ChEMBL; CHEMBL3085613; -.
DR   DrugCentral; P0C559; -.
DR   GeneID; 66738197; -.
DR   OMA; QLWSTTM; -.
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; IDA:UniProtKB.
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   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   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   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Topoisomerase.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..675
FT                   /note="DNA gyrase subunit B"
FT                   /id="PRO_0000145324"
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"
FT   CONFLICT        162
FT                   /note="G -> R (in Ref. 1; CAA58884)"
FT                   /evidence="ECO:0000305"
FT   HELIX           24..28
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   HELIX           31..34
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   HELIX           39..58
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          64..69
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          73..79
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          90..94
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   HELIX           95..101
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   HELIX           125..130
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          132..141
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          144..151
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          159..163
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          168..175
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   TURN            177..179
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   HELIX           187..200
FT                   /evidence="ECO:0007829|PDB:4BAE"
FT   STRAND          205..210
FT                   /evidence="ECO:0007829|PDB:4BAE"
SQ   SEQUENCE   675 AA;  74512 MW;  68A9B7F98BE07951 CRC64;
     MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV DNAVDEAMAG
     FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM TQLHAGGKFD GETYAVSGGL
     HGVGVSVVNA LSTRLEATVL RDGYEWFQYY DRSVPGKLKQ GGETKETGTT IRFWADPEIF
     ETTDYNFETV ARRLQEMAFL NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA
     TGPSKVKHRV FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES
     VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI REGLAAVISV
     KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP AEAKTVVNKA VSSAQARIAA
     RKARELVRRK SATDIGGLPG KLADCRSTDP SKSELYVVEG DSAGGSAKSG RDSMFQAILP
     LRGKIINVEK ARIDRVLKNT EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI
     STLLLTLLFR FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK
     INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI LMGEDVEARR
     SFITRNAKDV RFLDV
//