ID A0A929AN74_9CYAN Unreviewed; 1192 AA.
AC A0A929AN74;
DT 22-FEB-2023, integrated into UniProtKB/TrEMBL.
DT 22-FEB-2023, sequence version 1.
DT 18-JUN-2025, entry version 11.
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=IQ257_06455 {ECO:0000313|EMBL:MBE9148157.1};
OS Coleofasciculus sp. LEGE 07092.
OC Bacteria; Bacillati; Cyanobacteriota; Cyanophyceae; Coleofasciculales;
OC Coleofasciculaceae; Coleofasciculus.
OX NCBI_TaxID=2777969 {ECO:0000313|EMBL:MBE9148157.1, ECO:0000313|Proteomes:UP000619145};
RN [1] {ECO:0000313|EMBL:MBE9148157.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=LEGE 07092 {ECO:0000313|EMBL:MBE9148157.1};
RA Castelo-Branco R., Eusebio N., Adriana R., Vieira A.,
RA Brugerolle De Fraissinette N., Rezende De Castro R., Schneider M.P.,
RA Vasconcelos V., Leao P.N.;
RL Submitted (OCT-2020) to the EMBL/GenBank/DDBJ databases.
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}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01898}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:MBE9148157.1}.
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DR EMBL; JADEWY010000017; MBE9148157.1; -; Genomic_DNA.
DR RefSeq; WP_193873890.1; NZ_JADEWY010000017.1.
DR Proteomes; UP000619145; Unassembled WGS sequence.
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; IEA:UniProtKB-ARBA.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
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 GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR CDD; cd16928; HATPase_GyrB-like; 1.
DR CDD; cd00081; Hint; 1.
DR CDD; cd00093; HTH_XRE; 1.
DR CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR FunFam; 3.30.230.10:FF:000005; DNA gyrase subunit B; 1.
DR FunFam; 3.30.565.10:FF:000002; DNA gyrase subunit B; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
DR Gene3D; 2.170.16.10; Hedgehog/Intein (Hint) domain; 1.
DR Gene3D; 3.30.565.10; Histidine kinase-like ATPase, C-terminal domain; 1.
DR Gene3D; 3.10.28.10; Homing endonucleases; 1.
DR Gene3D; 1.10.260.40; lambda repressor-like DNA-binding domains; 1.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR001387; Cro/C1-type_HTH.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR027434; Homing_endonucl.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc_central.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR004860; LAGLIDADG_dom.
DR InterPro; IPR010982; Lambda_DNA-bd_dom_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_dom.
DR NCBIfam; TIGR01443; intein_Cterm; 1.
DR NCBIfam; TIGR01445; intein_Nterm; 1.
DR NCBIfam; NF004189; PRK05644.1; 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; PF01381; HTH_3; 1.
DR Pfam; PF14890; Intein_splicing; 1.
DR Pfam; PF14528; LAGLIDADG_3; 1.
DR Pfam; PF01751; Toprim; 1.
DR PRINTS; PR01159; DNAGYRASEB.
DR PRINTS; PR00379; INTEIN.
DR PRINTS; PR00418; TPI2FAMILY.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SMART; SM00530; HTH_XRE; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase; 1.
DR SUPFAM; SSF51294; Hedgehog/intein (Hint) domain; 1.
DR SUPFAM; SSF55608; Homing endonucleases; 1.
DR SUPFAM; SSF47413; lambda repressor-like DNA-binding domains; 1.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
DR SUPFAM; SSF56719; Type II DNA topoisomerase; 2.
DR PROSITE; PS50943; HTH_CROC1; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Autocatalytic cleavage {ECO:0000256|ARBA:ARBA00022813};
KW 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}; Protein splicing {ECO:0000256|ARBA:ARBA00023000};
KW Reference proteome {ECO:0000313|Proteomes:UP000619145};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 679..734
FT /note="HTH cro/C1-type"
FT /evidence="ECO:0000259|PROSITE:PS50943"
FT DOMAIN 806..939
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000259|PROSITE:PS50819"
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 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 1192 AA; 133506 MW; 6A4C1D8067EB630E CRC64;
MTSSYSADQI QVLEGLDPVR KRPGMYIGTT GPRGLHHLVY EVVDNSIDEA LAGYCTHIEV
DINAEGSVTV TDDGRGIPTD THPTTGKSAL ETVMTVLHAG GKFGGGGYKV SGGLHGVGVS
VVNALSEWVE VTVWREKLVH LQRYERGVPV TELTSKPNKQ DQTGTSVTFK PDTQIFTNGI
EFDYTTLAGR LRELAYLNAG VRMTFSDNRI SPPRVETYHY EGGIQEYVAY MNREKEPLHE
EIIYVQGERN NVQIEVALQW CIDAYSDNLL GFANNIRTID GGTHLEGLKT VLTRTMNAIA
RKRNKLKDNE ANLGGENVRE GLTGVISVKV PDPEFEGQTK TKLGNTEVRG IVDSLVGEVL
TEYLEFRPQV ADSVLEKAIQ AFKAAEAARR ARELVRRKSV LESSPLPGKL ADCSSRNPAD
SEIFIVEGDS AGGSAKQGRD RQFQAILPLR GKILNIEKTD DAKIYKNTEI QSLITALGLG
IKGEEFDASG LRYHRIVIMS VAGDEPTLVM DDTGRTEFVS IGGFIDDCIE ERRTTERYQV
ISFDPATHAT RFRPLKAVIR HGHEEPMYKI TTRYNRSVKV TSSHSVFVYE NGEVRLKKGN
EIKAGDLLVA SRRLPRPSEN PTRIDLLKTF YQAGLTQSLY LQGEDVRRIA SERVLAKVTR
PDQWNEPRVK LDLAGWQQLI AQRQAVGVSQ KQVATSVGVK QPITISHWER GINRPTLPHF
LSYLEVIGGN DNIVYETLPS KIDECLAQDD TSKNARWREV SCYKPFDYFT PSELAQLGDE
VELVPQAHSN KAFNRYLPIT QELMWFLGWY VAEGTLSKHQ VSLNLGKKDE RFIPELITAI
ESVFGETARC YNDPDSDGIK LYFHSVAAAR LLQAWGLAKC AHQKQLPDIL FSLGEEFQLT
FLEGYFLGDG TTGGKNLSFT TNSGTLKDGL LYLFGQLGLI ASTTEHQPAT AAEASIQTRH
SYYTITIGGK EQIKQYHQIW QRHSLAHKLE THLANPTRKA QDYVPISDDL MGLKVIAAEE
IEPVGEYVYD FSVEGDENFV CGTGGIACHN TDADVDGAHI RTLLLTFFYR YQRALVDQGY
IYIACPPLYK VERGRNHYYC YSDRELTNLV QHEFPANANY TIQRFKGLGE MMPTQLWDTT
MNPETRTMKR VEIEDAAEAD RIFTVLMGDR VAPRREFIET YGSRLNLTDL DI
//
