GYRBP_ARATH
ID GYRBP_ARATH Reviewed; 730 AA.
AC Q9SS38; F4J2L8;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 22-FEB-2012, sequence version 3.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=DNA gyrase subunit B, chloroplastic;
DE EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE Flags: Precursor;
GN Name=GYRBC; OrderedLocusNames=At3g10270; ORFNames=F14P13.13;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=15136745; DOI=10.1073/pnas.0400836101;
RA Wall M.K., Mitchenall L.A., Maxwell A.;
RT "Arabidopsis thaliana DNA gyrase is targeted to chloroplasts and
RT mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7821-7826(2004).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded DNA in an ATP-dependent manner.
CC {ECO:0000269|PubMed:15136745}.
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:15136745}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF02815.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC009400; AAF02815.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE74882.2; -; Genomic_DNA.
DR RefSeq; NP_001319516.1; NM_001337866.1.
DR AlphaFoldDB; Q9SS38; -.
DR SMR; Q9SS38; -.
DR BioGRID; 5523; 1.
DR STRING; 3702.AT3G10270.1; -.
DR PaxDb; Q9SS38; -.
DR ProteomicsDB; 247328; -.
DR EnsemblPlants; AT3G10270.1; AT3G10270.1; AT3G10270.
DR GeneID; 820189; -.
DR Gramene; AT3G10270.1; AT3G10270.1; AT3G10270.
DR KEGG; ath:AT3G10270; -.
DR Araport; AT3G10270; -.
DR eggNOG; KOG0355; Eukaryota.
DR InParanoid; Q9SS38; -.
DR PRO; PR:Q9SS38; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SS38; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
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 Nucleotide-binding; Plastid; Reference proteome; Topoisomerase;
KW Transit peptide.
FT TRANSIT 1..34
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 35..730
FT /note="DNA gyrase subunit B, chloroplastic"
FT /id="PRO_0000247948"
FT DOMAIN 511..618
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 517
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 591
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 591
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 593
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 542
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 545
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ SEQUENCE 730 AA; 81048 MW; 69B8F1295071C4B5 CRC64;
MALVQRQHSY LLRYFRLMAS RPRPRLFSHS LYPSLHRHSS ALSSSTPRIK FQLANVFSQR
LVQRNAVSPK SFMSSTMESL QESSTSKDYS SEHIQVLEGL DPVRKRPGMY IGSTGSRGLH
HLVYEILDNA IDEAQAGFAS KIDVVLHSDD SVSISDNGRG IPTDLHPATG KSSLETVLTV
LHAGGKFGGK SSGYSVSGGL HGVGLSVVNA LSEALEVIVR RDGMEFQQKY SRGKPVTTLT
CHVLPPESRG TQGTCIRFWP DKEVFTTAIQ FDHNTIAGRI RELAFLNPKV TISLKKEDDD
PERDVYSEYF YAGGLTEYVS WLNTDKKPLH DVLGFRKEIN GSTVDVSLQW CSDAYSDTML
GYANSIRTID GGTHIEGVKA SLTRTLNSLA KKLKVIKEKD ISLSGEHVRE GLTCIVSVKV
PNPEFEGQTK TRLGNPEVRK IVDQSVQEYL TEYLELHPDV LESIISKSLN AYKAALAAKR
ARELVRSKSV LKSSSLPGKL ADCSSTDPAE SEIFIVEGDS AGGSAKQGRD RRFQAILPLR
GKILNIERKD EAAMYKNEEI QNLILGLGLG VKGEDFNKEN LRYHKIIILT DADVDGAHIR
TLLLTFFFRY QRALFDAGCI YVGVPPLFKV ERGKQAHYCY DDAALKKITA SFPGNASYNI
QRFKGLGEMM PAQLWETTMN PDTRILKQLV VDDAAETNMV FSSLMGARVD VRKELIKSAA
TRMNLENLDI
