GYRB_MICLC
ID GYRB_MICLC Reviewed; 720 AA.
AC C5C7X8;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 86.
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:153201, ECO:0000269|PubMed:276855};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=Mlut_00050;
OS Micrococcus luteus (strain ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 /
OS NCIMB 9278 / NCTC 2665 / VKM Ac-2230) (Micrococcus lysodeikticus).
OC Bacteria; Actinobacteria; Micrococcales; Micrococcaceae; Micrococcus.
OX NCBI_TaxID=465515;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC
RC 2665 / VKM Ac-2230;
RX PubMed=19948807; DOI=10.1128/jb.01254-09;
RA Young M., Artsatbanov V., Beller H.R., Chandra G., Chater K.F., Dover L.G.,
RA Goh E.B., Kahan T., Kaprelyants A.S., Kyrpides N., Lapidus A., Lowry S.R.,
RA Lykidis A., Mahillon J., Markowitz V., Mavromatis K., Mukamolova G.V.,
RA Oren A., Rokem J.S., Smith M.C., Young D.I., Greenblatt C.L.;
RT "Genome sequence of the Fleming strain of Micrococcus luteus, a simple
RT free-living actinobacterium.";
RL J. Bacteriol. 192:841-860(2010).
RN [2]
RP FUNCTION IN NEGATIVE SUPERCOILING, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY
RP REGULATION, SUBUNIT, SUBCELLULAR LOCATION, AND DNA-BINDING.
RX PubMed=276855; DOI=10.1073/pnas.75.5.2098;
RA Liu L.F., Wang J.C.;
RT "Micrococcus luteus DNA gyrase: active components and a model for its
RT supercoiling of DNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 75:2098-2102(1978).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, SUBUNIT, AND
RP DNA-BINDING.
RX PubMed=153201; DOI=10.1016/0092-8674(78)90281-7;
RA Liu L.F., Wang J.C.;
RT "DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the
RT enzyme.";
RL Cell 15:979-984(1978).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils DNA in an
CC ATP-dependent manner (PubMed:276855). About 140 bp of DNA wraps around
CC gyrase in the presence or absence of ATP, when ATP is added negative
CC supercoils are made (PubMed:153201). {ECO:0000269|PubMed:153201,
CC ECO:0000269|PubMed:276855}.
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-Rule:MF_01898,
CC ECO:0000269|PubMed:153201, ECO:0000269|PubMed:276855};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:276855};
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: Supercoiling activity inhibited by novobiocin and
CC coumermycin, DNA wrapping around gyrase is not inhibited
CC (PubMed:153201, PubMed:276855). {ECO:0000269|PubMed:153201,
CC ECO:0000269|PubMed:276855}.
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC (PubMed:153201, PubMed:276855). In the heterotetramer, GyrA contains
CC the active site tyrosine that forms a transient covalent intermediate
CC with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.
CC {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:153201,
CC ECO:0000269|PubMed:276855}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:276855}.
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; CP001628; ACS29580.1; -; Genomic_DNA.
DR AlphaFoldDB; C5C7X8; -.
DR SMR; C5C7X8; -.
DR STRING; 465515.Mlut_00050; -.
DR PRIDE; C5C7X8; -.
DR EnsemblBacteria; ACS29580; ACS29580; Mlut_00050.
DR KEGG; mlu:Mlut_00050; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_11; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000000738; 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; IDA:UniProtKB.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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; 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..720
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000435542"
FT DOMAIN 498..612
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 504
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 577
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 577
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 579
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 529
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 532
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 720 AA; 78896 MW; 511E5C669610CBA7 CRC64;
MVDAMPENPA EEPTAASAAP NPEAVPDAVG QPEAPVKDRK VPGEYGASAI TVLEGLEAVR
KRPGMYIGST GPRGLHHLVY EVVDNSVDEA LAGYATGIDV TLQADGGVRV ADDGRGIPVD
LHPTEGRPTV EVVMTILHAG GKFGGGGYAV SGGLHGVGIS VVNALSRRVD TEVRRQGHVW
RMSFADGGVP QGELVKGEAT DATGTVQTFY PDAEIFDSIE FDYETLRARF QQMAFLNKGL
RITLTDERVQ ESNEVVDDEI AGEGAAGEDV AENGLAEDAE QEPQRRSVTY LYENGLLDYV
QHLNSAKKVE YVHDDVIAFE AEDFSDGRSM AVEVAMQWTS AYSESVHTYA NTINTHEGGT
HEEGFRAALT SLVNRYAREK EILKPKEDNL SGEDIREGLT AVISVKLSEP QFEGQTKTKL
GNSEARGFVS KAVTDHLGDW FERNPGPAKE IIRKAIMASH ARLAARKARD NARRKSPLES
FGMPGKLADC SSKDPERCEV YIVEGDSAGG SAKQGRNPET QAILPLRGKI LNVERARLDK
ALGNAEIQSM ITAFGTNIGE EFDISKLRYH KIVLMADADV DGQHITTLLL TVLFRYMRPL
IEAGHVFLAQ PPLYRIKWSN APHDYVFSDE ERDAAVEAGL AKGWRYPKDN GVQRYKGLGE
MNYQELWDTT MDPEHRTLLQ VTMEDAAAAD AVFSMLMGED VESRRTFIQQ NAKDIRFLDV
