ID   GYRB_NICBE              Reviewed;         731 AA.
AC   Q5YLB4;
DT   25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 68.
DE   RecName: Full=DNA gyrase subunit B, chloroplastic/mitochondrial;
DE            EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE   Flags: Precursor;
GN   Name=GYRB;
OS   Nicotiana benthamiana.
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae;
OC   Nicotiana.
OX   NCBI_TaxID=4100;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE
RP   SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX   PubMed=15367714; DOI=10.1105/tpc.104.024281;
RA   Cho H.S., Lee S.S., Kim K.D., Hwang I., Lim J.-S., Park Y.-I., Pai H.-S.;
RT   "DNA gyrase is involved in chloroplast nucleoid partitioning.";
RL   Plant Cell 16:2665-2682(2004).
CC   -!- FUNCTION: Seems to play a critical role in chloroplast nucleoid
CC       partitioning by regulating DNA topology. A type II topoisomerase that
CC       negatively supercoils closed circular double-stranded DNA in an ATP-
CC       dependent manner. {ECO:0000269|PubMed:15367714}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP-dependent breakage, passage and rejoining of double-
CC         stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|PROSITE-
CC         ProRule:PRU00995};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
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:0000255|PROSITE-
CC       ProRule:PRU00995};
CC   -!- SUBUNIT: Made up of two chains. The A chain is responsible for DNA
CC       breakage and rejoining; the B chain catalyzes ATP hydrolysis.
CC       {ECO:0000250|UniProtKB:P0AES6}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC       {ECO:0000269|PubMed:15367714}. Mitochondrion
CC       {ECO:0000269|PubMed:15367714}.
CC   -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:15367714}.
CC   -!- DEVELOPMENTAL STAGE: Up-regulated during seed germination and leaf
CC       expansion. {ECO:0000269|PubMed:15367714}.
CC   -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC       {ECO:0000305}.
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DR   EMBL; AY351387; AAR07943.1; -; mRNA.
DR   AlphaFoldDB; Q5YLB4; -.
DR   SMR; Q5YLB4; -.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0005694; C:chromosome; IEA:InterPro.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR   CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR   Gene3D; 3.30.230.10; -; 1.
DR   Gene3D; 3.30.565.10; -; 1.
DR   Gene3D; 3.40.50.670; -; 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_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   InterPro; IPR034160; TOPRIM_GyrB.
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; SM00433; TOP2c; 1.
DR   SUPFAM; SSF54211; SSF54211; 1.
DR   SUPFAM; SSF55874; SSF55874; 1.
DR   SUPFAM; SSF56719; SSF56719; 1.
DR   TIGRFAMs; TIGR01059; gyrB; 1.
DR   PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   2: Evidence at transcript level;
KW   ATP-binding; Chloroplast; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW   Mitochondrion; Nucleotide-binding; Plastid; Topoisomerase; Transit peptide.
FT   TRANSIT         1..?
FT                   /note="Chloroplast and mitochondrion"
FT   CHAIN           ?..731
FT                   /note="DNA gyrase subunit B, chloroplastic/mitochondrial"
FT                   /id="PRO_0000247950"
FT   DOMAIN          512..619
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         518
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         592
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         592
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   BINDING         594
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            543
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            546
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ   SEQUENCE   731 AA;  81600 MW;  7D4DD34D4EA16C10 CRC64;
     MALLKPFPLQ HSLRCMASRF LLHSHYHTHT LSFSSISLSR PSIVLNPRVI NKLRRLSDAI
     LIRNMVSLRA FMSSSTTTEA FQENTKSKGY GSEQIQVLEG LDPVRKRPGM YIGSTGPRGL
     HHLVYEILDN AVDEAQAGFA TKIDVVLHAD NSVSIADNGR GIPTELHPVT KKSSLETVLT
     VLHAGGKFGG SSSGYNVSGG LHGVGLSVVN ALSQALEVTI WRDGKEYQQK YSRGKPITTL
     ICHDLPVEMR DRQGTAIRFW PDKEVFTTEM QFDYNTIAGR IRELAFLNPE LTIALKKEDI
     DPEKIQCNEY FYAGGLVEYV KWLNADKKPL HDVLGFRKEA DGITIDMALQ WCSDAYSDTM
     LGYANSIRTI DGGTHIDGVK AALTRILNNL GKKSKTIKEK DISLSGEHVR EGLTCVISVK
     VPNPEFEGQT KTRLGNPEVR KVVDQSVQEY LTEYLELHPD VLDSILSKSL NALKAALAAK
     RARELVRQKS VLKSSSLPGK LADCSATNPE EAEIFIVEGD SAGGSAKQGR DRRFQAILPL
     RGKILNIERK DEAAMYKNEE IQNLILGLGL GVKGEDFKKE ALRYHKIIIL TDADVDGAHI
     RTLLLTFFFR YQRALFEEGC IYVGVPPLYK VERGKQVYYC YDDAELKKVQ RSFPSNASYN
     IQRFKGLGEM MPAQLWETTM NPETRLLKQL VVEDAAEANV VFSSLMGSRV DIRKQLIQNS
     ASMMNLEQLD I