ID B6AMY5_9BACT Unreviewed; 818 AA.
AC B6AMY5;
DT 25-NOV-2008, integrated into UniProtKB/TrEMBL.
DT 25-NOV-2008, sequence version 1.
DT 24-JAN-2024, entry version 79.
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 ORFNames=CGL2_11386003 {ECO:0000313|EMBL:EDZ39817.1};
OS Leptospirillum sp. Group II '5-way CG'.
OC Bacteria; Nitrospirota; Nitrospiria; Nitrospirales; Nitrospiraceae;
OC Leptospirillum.
OX NCBI_TaxID=419541 {ECO:0000313|EMBL:EDZ39817.1};
RN [1] {ECO:0000313|EMBL:EDZ39817.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=14961025; DOI=10.1038/nature02340;
RA Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J.,
RA Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., Banfield J.F.;
RT "Community structure and metabolism through reconstruction of microbial
RT genomes from the environment.";
RL Nature 428:37-43(2004).
RN [2] {ECO:0000313|EMBL:EDZ39817.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=18651792; DOI=10.1371/journal.pbio.0060177;
RA Simmons S.L., Dibartolo G., Denef V.J., Goltsman D.S., Thelen M.P.,
RA Banfield J.F.;
RT "Population genomic analysis of strain variation in Leptospirillum group II
RT bacteria involved in acid mine drainage formation.";
RL PLoS Biol. 6:E177-E177(2008).
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; DS995259; EDZ39817.1; -; Genomic_DNA.
DR AlphaFoldDB; B6AMY5; -.
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; -; 2.
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; IPR049353; GyrB_hook.
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; PF21249; GyrB_hook; 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};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, 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};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 421..537
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 427
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 502
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 502
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 504
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 452
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 455
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 818 AA; 92222 MW; 35EEE0F9EACCF224 CRC64;
MSSGEPVEEE YTAEHIRVLE GLEAVRVRPG MYIGSTGIDG LHHLVYELVD NSVDEALAGH
CSEIHVTIHP DRSVTVADNG RGIPTGMHAE QKRSAAEVVL TVLHAGGKFN NNLYKVSGGL
HGVGVSVVNA LSETLFLEIH QNGLIHRQTY HKGAPDAPLA VFGETAQRGT IIRFWPDMTI
METDQFSFDT LSHRFRELAF LNPVLTIHLK EEETLREETF HFEGGVQSFV SFLNENKKTL
HDVLFFRKTL EDGSQFEVAF QYQESTENET VLGFANNIHT REGGTHVRGF RTAITKTINR
FIREKQLNKG EEVRGEDVRE GLTGIISVRI PGPQFEGQTK AKLGSSWVAG AMESFLSEAL
QEKFEEDPLT AKKIAEKAVL TAQAREAARK AKDLAKRKNV LEGSNLPGKL ADCQESDPAK
SELYIVEGDS AGGSAKQGRD RRFQAILPLK GKILNVEKSR GIEKFITNDE VRALITAVGC
GLGEEEFSEK KLRYHKIIIM TDADVDGAHI RTLLLTFFFR HMNPLIDGQF VYIAQPPLYK
VSYGRQERYL LNDEALQAYI LELACADWMF YDEQAGHWLA REEAVAKLLV LVHFEEQVRA
HAQRFGNEML LRLIGMFTET GIEVLKSEEA ARRLVSFLTG EYPGWVAGGR LDGQVERDPV
MAETHPEEEW FRIRFFTESL GYESRLVLDH YLLAQLLAGK RSLRLLRQSG LLFPGGFVLK
RGAEGEEVRF RSPRELLSFL ETPVRQKLSI QRYKGLGEMN PEQLWETTMD PSRRTLLKVS
IPDYVEADRV FTTLMGEQVA PRREFIEKHA LDVANLDI
//
