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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:12000834};
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 -!- 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
//
