ID Q03D51_LACP3 Unreviewed; 653 AA.
AC Q03D51;
DT 14-NOV-2006, integrated into UniProtKB/TrEMBL.
DT 14-NOV-2006, sequence version 1.
DT 27-MAR-2024, entry version 129.
DE RecName: Full=DNA gyrase subunit B {ECO:0000256|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000256|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898};
GN OrderedLocusNames=LSEI_0005 {ECO:0000313|EMBL:ABJ68871.1};
OS Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 /
OS CIP 107868 / KCTC 3260 / NRRL B-441) (Lactobacillus paracasei).
OC Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
OC Lacticaseibacillus.
OX NCBI_TaxID=321967 {ECO:0000313|EMBL:ABJ68871.1, ECO:0000313|Proteomes:UP000001651};
RN [1] {ECO:0000313|EMBL:ABJ68871.1, ECO:0000313|Proteomes:UP000001651}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 /
RC NRRL B-441 {ECO:0000313|Proteomes:UP000001651};
RX PubMed=17030793; DOI=10.1073/pnas.0607117103;
RA Makarova K., Slesarev A., Wolf Y., Sorokin A., Mirkin B., Koonin E.,
RA Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V.,
RA Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M.,
RA Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A.,
RA Baldwin K., Lee J.H., Diaz-Muniz I., Dosti B., Smeianov V., Wechter W.,
RA Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y.,
RA Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J., Hutkins R.,
RA O'Sullivan D., Steele J., Unlu G., Saier M., Klaenhammer T., Richardson P.,
RA Kozyavkin S., Weimer B., Mills D.;
RT "Comparative genomics of the lactic acid bacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
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:0000256|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:0000256|ARBA:ARBA00000185,
CC ECO:0000256|HAMAP-Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|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:0000256|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000256|ARBA:ARBA00010708, ECO:0000256|HAMAP-Rule:MF_01898}.
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DR EMBL; CP000423; ABJ68871.1; -; Genomic_DNA.
DR RefSeq; WP_011673927.1; NC_008526.1.
DR RefSeq; YP_805313.1; NC_008526.1.
DR AlphaFoldDB; Q03D51; -.
DR STRING; 321967.LSEI_0005; -.
DR PaxDb; 321967-LSEI_0005; -.
DR KEGG; lca:LSEI_0005; -.
DR PATRIC; fig|321967.11.peg.40; -.
DR HOGENOM; CLU_006146_4_1_9; -.
DR Proteomes; UP000001651; 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; 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 {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01898};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01898};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01898};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Reference proteome {ECO:0000313|Proteomes:UP000001651};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 435..549
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 441
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 514
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 514
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 516
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 469
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 653 AA; 72486 MW; 6574037969C1C935 CRC64;
MTDKKETAEE KKDELAAEYD ASQIQVLSGL EAVRKRPGMY IGSTSSQGLH HLVWEIIDNG
IDEALAGFAT RIEVEVNPDN SVTVTDDGRG IPVDIQSKTG RPALETVYTV LHAGGKFGGG
GYKVSGGLHG VGASVVNALS TDLDVTVTRG GKRYYIDFIR GKVNMPMKVI GTAPEHEHGT
KVHFLPDPDI FTEIRTFDDK ILTTRIRELA FLNKGLKLTF TDKRAATHEK LVFHYEGGLK
SYVDFLTEKK ENLLQEPIYV EGQDKGITVE VALQYTNDYH STLLTFANNI HTYEGGTHET
GFKTALTRVI NDYARRSGAL KDSDDPLSGD DVREGLTAVV SVKHPDPQFE GQTKTKLGNS
DARTVVDRTF SDHFNKFLME HPADGKLIID KAMLASKARL AAKRAREVTR KKSGLEISNL
PGKLADNTSK DPEISELFIV EGDSAGGSAK SGRSRLTQAI LPIRGKILNV EKASMERILA
NEEIRTLFTA MGTGFGQDFD INKARYHKLI IMTDADVDGA HIRTLLLTLI YRYMRPVLDA
GYVYIAQPPL YRLRQGKMTQ YIDSDEELQD ILGQLPPSPK PEIQRYKGLG EMDANQLWET
TMDPDNRRLL RVSPKDAEAA DGVFEMLMGD HVEPRRKFIE DNAVFVDPNN IDA
//
