GYRB_STRR6
ID GYRB_STRR6 Reviewed; 648 AA.
AC P0A4M0; P48373;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 105.
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=spr0715;
OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=171101;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001;
RA Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
RA DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
RA Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J.,
RA Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M.,
RA McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B.,
RA Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y.,
RA Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R.,
RA Rosteck P.R. Jr., Skatrud P.L., Glass J.I.;
RT "Genome of the bacterium Streptococcus pneumoniae strain R6.";
RL J. Bacteriol. 183:5709-5717(2001).
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE007317; AAK99519.1; -; Genomic_DNA.
DR PIR; C97961; C97961.
DR RefSeq; NP_358309.1; NC_003098.1.
DR RefSeq; WP_000134039.1; NC_003098.1.
DR PDB; 4Z2C; X-ray; 3.19 A; C/D=404-648.
DR PDB; 4Z2D; X-ray; 3.38 A; C/D=404-648.
DR PDB; 4Z2E; X-ray; 3.46 A; C/D=404-648.
DR PDBsum; 4Z2C; -.
DR PDBsum; 4Z2D; -.
DR PDBsum; 4Z2E; -.
DR AlphaFoldDB; P0A4M0; -.
DR SMR; P0A4M0; -.
DR STRING; 171101.spr0715; -.
DR EnsemblBacteria; AAK99519; AAK99519; spr0715.
DR GeneID; 60234325; -.
DR KEGG; spr:spr0715; -.
DR PATRIC; fig|171101.6.peg.791; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_9; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000000586; 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 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 3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..648
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145348"
FT DOMAIN 427..541
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 433
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 506
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 506
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 461
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT TURN 424..426
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 428..433
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 434..442
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 443..445
FT /evidence="ECO:0007829|PDB:4Z2C"
FT TURN 447..449
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 450..455
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 462..464
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 467..470
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 474..483
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 493..495
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 501..504
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 509..525
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 527..532
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 535..538
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 592..599
FT /evidence="ECO:0007829|PDB:4Z2C"
FT TURN 602..604
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 606..611
FT /evidence="ECO:0007829|PDB:4Z2C"
FT HELIX 615..625
FT /evidence="ECO:0007829|PDB:4Z2C"
FT STRAND 626..628
FT /evidence="ECO:0007829|PDB:4Z2E"
FT HELIX 630..639
FT /evidence="ECO:0007829|PDB:4Z2C"
SQ SEQUENCE 648 AA; 72238 MW; 976A0B030BC892C4 CRC64;
MTEEIKNLQA QDYDASQIQV LEGLEAVRMR PGMYIGSTSK EGLHHLVWEI VDNSIDEALA
GFASHIQVFI EPDDSITVVD DGRGIPVDIQ EKTGRPAVET VFTVLHAGGK FGGGGYKVSG
GLHGVGSSVV NALSTQLDVH VHKNGKIHYQ EYRRGHVVAD LEIVGDTDKT GTTVHFTPDP
KIFTETTIFD FDKLNKRIQE LAFLNRGLQI SITDKRQGLE QTKHYHYEGG IASYVEYINE
NKDVIFDTPI YTDGEMDDIT VEVAMQYTTG YHENVMSFAN NIHTHEGGTH EQGFRTALTR
VINDYARKNK LLKDNEDNLT GEDVREGLTA VISVKHPNPQ FEGQTKTKLG NSEVVKITNR
LFSEAFSDFL MENPQIAKRI VEKGILAAKA RVAAKRAREV TRKKSGLEIS NLPGKLADCS
SNNPAETELF IVEGDSAGGS AKSGRNREFQ AILPIRGKIL NVEKASMDKI LANEEIRSLF
TAMGTGFGAE FDVSKARYQK LVLMTDADVD GAHIRTLLLT LIYRYMKPIL EAGYVYIAQP
PIYGVKVGSE IKEYIQPGAD QEIKLQEALA RYSEGRTKPT IQRYKGLGEM DDHQLWETTM
DPEHRLMARV SVDDAAEADK IFDMLMGDRV EPRREFIEEN AVYSTLDV
