ID C6XFY4_LIBAP Unreviewed; 803 AA.
AC C6XFY4;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 27-MAR-2024, entry version 99.
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 ECO:0000313|EMBL:ACT57287.1};
GN OrderedLocusNames=CLIBASIA_03525 {ECO:0000313|EMBL:ACT57287.1};
OS Liberibacter asiaticus (strain psy62).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Liberibacter.
OX NCBI_TaxID=537021 {ECO:0000313|EMBL:ACT57287.1, ECO:0000313|Proteomes:UP000002744};
RN [1] {ECO:0000313|EMBL:ACT57287.1, ECO:0000313|Proteomes:UP000002744}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=psy62 {ECO:0000313|Proteomes:UP000002744};
RX PubMed=19589076; DOI=10.1094/MPMI-22-8-1011;
RA Duan Y., Zhou L., Hall D.G., Li W., Doddapaneni H., Lin H., Liu L.,
RA Vahling C.M., Gabriel D.W., Williams K.P., Dickerman A., Sun Y.,
RA Gottwald T.;
RT "Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus
RT Liberibacter asiaticus' obtained through metagenomics.";
RL Mol. Plant Microbe Interact. 22:1011-1020(2009).
RN [2] {ECO:0000313|EMBL:ACT57287.1, ECO:0000313|Proteomes:UP000002744}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=psy62 {ECO:0000313|Proteomes:UP000002744};
RX PubMed=21784907; DOI=10.1128/AEM.05111-11;
RA Zhou L., Powell C.A., Hoffman M.T., Li W., Fan G., Liu B., Lin H., Duan Y.;
RT "Diversity and plasticity of the intracellular plant pathogen and insect
RT symbiont, 'Candidatus Liberibacter asiaticus', revealed by hyper variable
RT prophage genes with intragenic tandem repeats.";
RL Appl. Environ. Microbiol. 77:6663-6673(2011).
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; CP001677; ACT57287.1; -; Genomic_DNA.
DR RefSeq; WP_012778728.1; NC_012985.3.
DR AlphaFoldDB; C6XFY4; -.
DR STRING; 537021.CLIBASIA_03525; -.
DR GeneID; 66285984; -.
DR KEGG; las:CLIBASIA_03525; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_5; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000002744; 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; -; 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; 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};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 425..540
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 431
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 505
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 505
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 507
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 456
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 459
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 803 AA; 89734 MW; FD0B7568E41FBF0C CRC64;
MSDNIQNSSY DADSIQILKG LDAVKKRPSM YIGDTDGESG LHHMIYEVLD NAIDESLEGY
ADIITVTLNM DGSCTVSDNG RGIPTDLHKE EGISAAEVIM TRLHAGGKFN QKSYKVSGGL
HGVGVSVVNA LSSWLKLRIK REGNIYEMSF INGILDNPLV VTGSAGNDTG TEVTFLPSSD
IFSVQDFNYD TLQHRLRELS FLNSSVQISL IDKRSPEPRE ITMFYKGGIE AFVSYLDRHK
KPLMQSPIRI QGSRDNISID LAMRWNDGYH ENVLCFTNNI PQKDGGTHLS GLRSALTRQI
TSYVEKSFGS KKDKRSVIGD DCREGFTSVL SIKMPDPRFS SQTKEKLVSS EVRSVVESFV
NDGLSAWLEE HPLEAKIIVK KVLDASMVRD AARRARDLTR RKGVLDIASL PGKLADCSER
DPKKSELFLV EGDSAGGSAK QGRSRENQAI LPLRGKILNV ERARFDKMLS SQEIGTLITA
LGTGIGQDSF DINKLRYHKI IIMTDADVDG AHIRTLLLTF FFRQMPSLIH NGFLYIIKPP
LYGITRGKSL QYVKDEESLE DYLINQSLSE EIELFCDSKG VISKNDLRNF IDDALKIDKL
IKDFYPNHDK TFIEQAVISG VFNCESDQEI NVSLASKLAN RLNFIAEKSE KSWHGSINNS
DILVKRIARG VQEQFVLEGS SIFSFGSKYK RIFSNRIEEN YLTILSLICN GDKIKITGPC
SLLDTIFSIG RKGISMQRYK GLGEMNASQL WETTLNPDTR SLLRVKITDA SQADDLFSRL
MGDEVEPRRE FIQENSLPSA LDI
//
