GYRBM_ARATH
ID GYRBM_ARATH Reviewed; 732 AA.
AC Q94BZ7; Q3E9M5; Q9FYE7;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DNA gyrase subunit B, mitochondrial;
DE EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE Flags: Precursor;
GN Name=GYRBM; OrderedLocusNames=At5g04130; ORFNames=F21E1_50;
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
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: Mitochondrion {ECO:0000269|PubMed:15136745}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q94BZ7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q94BZ7-2; Sequence=VSP_020235, VSP_020236;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to an intron retention.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC05495.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL391716; CAC05495.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED90701.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90702.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM68979.1; -; Genomic_DNA.
DR EMBL; AY039521; AAK62578.1; -; mRNA.
DR EMBL; AY142041; AAM98305.1; -; mRNA.
DR RefSeq; NP_001318477.1; NM_001342753.1. [Q94BZ7-2]
DR RefSeq; NP_568133.1; NM_120495.3. [Q94BZ7-1]
DR RefSeq; NP_850762.1; NM_180431.2. [Q94BZ7-2]
DR AlphaFoldDB; Q94BZ7; -.
DR SMR; Q94BZ7; -.
DR STRING; 3702.AT5G04130.1; -.
DR PaxDb; Q94BZ7; -.
DR PRIDE; Q94BZ7; -.
DR ProteomicsDB; 247327; -. [Q94BZ7-1]
DR EnsemblPlants; AT5G04130.1; AT5G04130.1; AT5G04130. [Q94BZ7-1]
DR EnsemblPlants; AT5G04130.2; AT5G04130.2; AT5G04130. [Q94BZ7-2]
DR EnsemblPlants; AT5G04130.3; AT5G04130.3; AT5G04130. [Q94BZ7-2]
DR GeneID; 830291; -.
DR Gramene; AT5G04130.1; AT5G04130.1; AT5G04130. [Q94BZ7-1]
DR Gramene; AT5G04130.2; AT5G04130.2; AT5G04130. [Q94BZ7-2]
DR Gramene; AT5G04130.3; AT5G04130.3; AT5G04130. [Q94BZ7-2]
DR KEGG; ath:AT5G04130; -.
DR Araport; AT5G04130; -.
DR TAIR; locus:2146698; AT5G04130.
DR eggNOG; KOG0355; Eukaryota.
DR HOGENOM; CLU_006146_4_1_1; -.
DR InParanoid; Q94BZ7; -.
DR OMA; YHLTGFK; -.
DR OrthoDB; 514092at2759; -.
DR PhylomeDB; Q94BZ7; -.
DR PRO; PR:Q94BZ7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94BZ7; baseline and differential.
DR Genevisible; Q94BZ7; AT.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
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 Alternative splicing; ATP-binding; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Mitochondrion; Nucleotide-binding; Reference proteome;
KW Topoisomerase; Transit peptide.
FT TRANSIT 1..?
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN ?..732
FT /note="DNA gyrase subunit B, mitochondrial"
FT /id="PRO_0000247949"
FT DOMAIN 513..620
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 519
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 593
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 593
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 595
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 544
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 547
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT VAR_SEQ 514..519
FT /note="EIFIVE -> GMYWPS (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_020235"
FT VAR_SEQ 520..732
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_020236"
SQ SEQUENCE 732 AA; 81053 MW; 059EF1601E779189 CRC64;
MALLQRASYL RLYYLRLMGS RPRLFSSSLS PALHRHSSTL SSPPFSSPSP SFRLKFQLTS
VLSQRLIQRN AISSRFLSTE ASQETTTSKG YSSEQIQVLE GLDPVRKRPG MYIGSTGSRG
LHHLVYEILD NAIDEAQAGY ASKVDVVLHA DGSVSVVDNG RGIPTDLHPA TKKSSLETVL
TVLHAGGKFG GTSSGYSVSG GLHGVGLSVV NALSEALEVS VWRDGMEHKQ NYSRGKPITT
LTCRVLPLES KGTKGTSIRF WPDKEVFTTA IEFDHNTIAG RIRELAFLNP KVTISLKKED
DDPEKTQYSE YSFAGGLTEY VSWLNTDKNP IHDVLGFRRE INGATVDVAL QWCSDAYSDT
MLGYANSIRT IDGGTHIEGV KASLTRTLNT LAKKSKTVKE KDISLSGEHV REGLTCIVSV
KVPNPEFEGQ TKTRLGNPEV RKIVDQSVQE YLTEFLELHP DILESIISKS LNAYKAALAA
KRARELVRSK SVLKSSSLPG KLADCSSTDP EVSEIFIVEG DSAGGSAKQG RDRRFQAILP
LRGKILNIER KDEAAMYKNE EIQNLILGLG LGVKGEDFKK ENLRYHKIII LTDADVDGAH
IRTLLLTFFF RYQRALFDAG CIYVGVPPLF KVERGKNAQY CYDDADLKKI TSNFPANASY
NIQRFKGLGE MMPEQLWETT MNPETRILKQ LVVDDIAEAN MTFSSLMGAR VDVRKELIKN
AATRINLQRL DI
