GYRB_SYNY3
ID GYRB_SYNY3 Reviewed; 1078 AA.
AC P77966;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=DNA gyrase subunit B;
DE EC=5.6.2.2 {ECO:0000250|UniProtKB:P0AES6};
DE Contains:
DE RecName: Full=Ssp GyrB intein;
GN Name=gyrB; OrderedLocusNames=sll2005;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
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.
CC {ECO:0000250|UniProtKB:P0AES6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000250|UniProtKB:P0AES6};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00995};
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:0000250|UniProtKB:P0AES6}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P0AES6}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
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:0000305}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000305}.
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DR EMBL; BA000022; BAA17720.1; -; Genomic_DNA.
DR PIR; S77162; S77162.
DR AlphaFoldDB; P77966; -.
DR SMR; P77966; -.
DR DIP; DIP-48809N; -.
DR IntAct; P77966; 16.
DR STRING; 1148.1652801; -.
DR PaxDb; P77966; -.
DR PRIDE; P77966; -.
DR EnsemblBacteria; BAA17720; BAA17720; BAA17720.
DR KEGG; syn:sll2005; -.
DR eggNOG; COG0187; Bacteria.
DR eggNOG; COG1372; Bacteria.
DR InParanoid; P77966; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; P77966; -.
DR Proteomes; UP000001425; 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-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR003594; HATPase_C.
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; IPR030934; Intein_C.
DR InterPro; IPR006141; Intein_N.
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 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; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 2.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding; Cytoplasm; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..1078
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000435539"
FT CHAIN 1..436
FT /note="DNA gyrase subunit B, 1st part"
FT /id="PRO_0000034816"
FT CHAIN 437..871
FT /note="Ssp GyrB intein"
FT /id="PRO_0000034817"
FT CHAIN 872..1078
FT /note="DNA gyrase subunit B, 2nd part"
FT /id="PRO_0000034818"
FT DOMAIN 889..974
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 895
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 939
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 939
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 941
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ SEQUENCE 1078 AA; 122819 MW; 6CA02586DFEA607B CRC64;
MTMTTTNYGA DQIQVLEGLE PVRKRPGMYI GSTGPKGLHH LVYEVVDNAI DEALAGYCTH
IEIDINADGS VTVVDNGRGI PTDIHPTTGR SALETVLTVL HAGGKFGGGG YKVSGGLHGV
GVSVVNALSE WVEVKVWRQG KEHFQRFERG NPIGTLEATP NEGHSTGTQV SFLPDTQIFK
DGIEFDYHTL ASRLKELAYL NAGVRITFGD RRADSLKEEQ FYYEGGIREY VTYMTTDKTP
LHEEIIYTSG EKNDVQVEVA LQWCVDAYSD TLLGFANNIR TIDGGTHLEG LKAVLTRTLN
SVARKRNKLK DGDSNLGGEN IREGLTGVIS VKVPDPEFEG QTKTKLGNTE VRGIVDTLVG
EALTEFLEFN PGVADAIIEK AVQAFKAAEA ARRARELVRR KSVLESSTLP GKLADCSSKD
PSESEIFIVE GDSAGGCFSG DTLVALTDGR SVSFEQLVEE EKQGKQNFCY TIRHDGSIGV
EKIINARKTK TNAKVIKVTL DNGESIICTP DHKFMLRDGS YKCAMDLTLD DSLMPLHRKI
STTEDSGITI DGYEMVWSPR SDSWLFTHLV ADWYNRWQGI YIAEEKQHCH HKDFNKRNNN
PDNLIRLSPE KHLALHRKHI SKTLHRPDVV EKCRRIHQSP EFRRKMSARM QSPETRAILS
KQAQAQWQNE TYKLTMMESW RSFYDSNEDY RQQNAEQLNR AQQEYWAQAE NRTAQAERVR
QHFAQNPGLR QQYSENAVKQ WNNPELLKWR QKKTKEQWTP EFREKRREAL AQTYYRKTLA
ALKQVEIENG YLDISAYDSY RISTKDKSLL RFDRFCERYF ENDENLAREA VLNYNHRIVN
IEAVSETIDV YDIEVPHTHN FALASGVFVH NSAKQGRDRR FQAILPLRGK ILNIEKTDDA
KIYKNTEIQA LITALGLGIK GDDFDISSLR YHRVVIMTDA DVDGAHIRTL LLTFFYRYQR
DLVDQGYIYI ACPPLYKLER GKNHFYCYSD RELQEQISQF PPNANYTIQR FKGLGEMMPQ
QLWDTTMNPE SRTMKRVHIE DAAEADRIFT VLMGDRVAPR REFIETYGTK LDLTDLDI
