GYRB_ORYSJ
ID GYRB_ORYSJ Reviewed; 729 AA.
AC Q5NBJ3; Q0JNS3;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 103.
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; OrderedLocusNames=Os01g0268300, LOC_Os01g16290;
GN ORFNames=P0011D01.27, P0667A10.1;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded DNA in an ATP-dependent manner.
CC {ECO:0000250|UniProtKB:Q94BZ7}.
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 {ECO:0000305}. Mitochondrion
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000305}.
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DR EMBL; AP000969; BAD81142.1; -; Genomic_DNA.
DR EMBL; AP001073; BAD81163.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF04605.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS71481.1; -; Genomic_DNA.
DR EMBL; AK102391; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015622284.1; XM_015766798.1.
DR AlphaFoldDB; Q5NBJ3; -.
DR SMR; Q5NBJ3; -.
DR STRING; 4530.OS01T0268300-01; -.
DR PaxDb; Q5NBJ3; -.
DR PRIDE; Q5NBJ3; -.
DR EnsemblPlants; Os01t0268300-01; Os01t0268300-01; Os01g0268300.
DR GeneID; 4326261; -.
DR Gramene; Os01t0268300-01; Os01t0268300-01; Os01g0268300.
DR KEGG; osa:4326261; -.
DR eggNOG; KOG0355; Eukaryota.
DR HOGENOM; CLU_006146_4_1_1; -.
DR InParanoid; Q5NBJ3; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 514092at2759; -.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR ExpressionAtlas; Q5NBJ3; baseline and differential.
DR Genevisible; Q5NBJ3; OS.
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; Reference proteome;
KW Topoisomerase; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast and mitochondrion"
FT CHAIN ?..729
FT /note="DNA gyrase subunit B, chloroplastic/mitochondrial"
FT /id="PRO_0000247951"
FT DOMAIN 510..617
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 516
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 590
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 590
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
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 SITE 541
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 544
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT CONFLICT 81
FT /note="Q -> R (in Ref. 5; AK102391)"
FT /evidence="ECO:0000305"
FT CONFLICT 378
FT /note="K -> R (in Ref. 5; AK102391)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 729 AA; 80469 MW; 0C03512014D79596 CRC64;
MGPLLRSSPP PRHLRLLLRR LLSTAAGRPS RLLPLPASSS ARLLVRPRVA VAAAAAGAPL
RRNGVAVRAF MASTAASEAM QEKRVAGEYT AANVQVLEAL DGVRTRPGMY IGSTGSRGLH
HLVYEILDNA VDEAQAGYAT KVDVILHGDN SVSVTDNGRG IPTDIHPQTK KSCVETVLTL
MHAGGKFGGS KSGYTVSGGL HGVGLSVVNA LSEALEVTVW RDGKEYRQNY SRGKAITMLT
SRTLSDESSS RQGTRIRFWP DKHIFTTTMD FDFNTIAGRI RELAFLNPEL TIALTKEEDD
LQVQHNEYCY AGGLVEYVKW LNTDKKSLHD PIAFRKEMDG ITVDVSLQWC SDSYSDTVLG
YANSIRTIDG GTHIDGLKTS LTRTINNFAK KSKTLKDKDI SLSGEHVREG MTCIIAVKVP
NPEFEGQTKT RLGNPEVRRI VEQSVQENLT EYLELHPDVL DSILSKSLNA LKAALAAKRA
RELVRTKSVL KSSSLPGKLA DCASSDPEES EIFIVEGDSA GGSAKQGRDR KFQAILPLRG
KILNIERRDE AALYKNEEIQ NLIVALGLGV KGEDFNKEAL RYHKIVILTD ADVDGAHIRT
LLLTFFFRYQ KALFDEGCIY VGVPPLYKVE RGKQAHYCYD DADLKELVNT FPTNASYHIQ
RFKGLGEMMP AQLWETTMDP ERRMLKQLKV EDAAEANVVF SSLMGTRVDV RKQLIQNAAS
MVNLEHLDI
