TOP3B_ARATH
ID TOP3B_ARATH Reviewed; 865 AA.
AC F4ISQ7; Q56YZ6; Q680E4; Q9SKZ9;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=DNA topoisomerase 3-beta;
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10131};
GN OrderedLocusNames=At2g32000; ORFNames=F22D22.25;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA
CC introduced during the DNA replication and transcription by transiently
CC cleaving and rejoining one strand of the DNA duplex. Introduces a
CC single-strand break via transesterification at a target site in duplex
CC DNA. The scissile phosphodiester is attacked by the catalytic tyrosine
CC of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-
CC enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free
CC DNA strand than undergoes passage around the unbroken strand thus
CC removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH
CC attacks the covalent intermediate to expel the active-site tyrosine and
CC restore the DNA phosphodiester backbone (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10131};
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 -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=F4ISQ7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4ISQ7-2; Sequence=VSP_055207;
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD15404.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC006223; AAD15404.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC08619.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC08620.1; -; Genomic_DNA.
DR EMBL; AK175789; BAD43552.1; -; mRNA.
DR EMBL; AK175923; BAD43686.1; -; mRNA.
DR EMBL; AK221174; BAD95240.1; -; mRNA.
DR PIR; G84727; G84727.
DR RefSeq; NP_001031463.1; NM_001036386.1. [F4ISQ7-2]
DR RefSeq; NP_180760.2; NM_128760.4. [F4ISQ7-1]
DR AlphaFoldDB; F4ISQ7; -.
DR SMR; F4ISQ7; -.
DR STRING; 3702.AT2G32000.1; -.
DR PaxDb; F4ISQ7; -.
DR PRIDE; F4ISQ7; -.
DR ProteomicsDB; 234443; -. [F4ISQ7-1]
DR EnsemblPlants; AT2G32000.1; AT2G32000.1; AT2G32000. [F4ISQ7-1]
DR EnsemblPlants; AT2G32000.2; AT2G32000.2; AT2G32000. [F4ISQ7-2]
DR GeneID; 817760; -.
DR Gramene; AT2G32000.1; AT2G32000.1; AT2G32000. [F4ISQ7-1]
DR Gramene; AT2G32000.2; AT2G32000.2; AT2G32000. [F4ISQ7-2]
DR KEGG; ath:AT2G32000; -.
DR Araport; AT2G32000; -.
DR TAIR; locus:2045517; AT2G32000.
DR eggNOG; KOG1957; Eukaryota.
DR HOGENOM; CLU_002929_1_0_1; -.
DR InParanoid; F4ISQ7; -.
DR OMA; TYPRVDT; -.
DR PRO; PR:F4ISQ7; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; F4ISQ7; baseline and differential.
DR Genevisible; F4ISQ7; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003916; F:DNA topoisomerase activity; IBA:GO_Central.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; HDA:TAIR.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1.
DR Gene3D; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 2.70.20.10; -; 1.
DR InterPro; IPR000380; Topo_IA.
DR InterPro; IPR003601; Topo_IA_2.
DR InterPro; IPR023406; Topo_IA_AS.
DR InterPro; IPR013497; Topo_IA_cen.
DR InterPro; IPR013824; Topo_IA_cen_sub1.
DR InterPro; IPR013825; Topo_IA_cen_sub2.
DR InterPro; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034144; TOPRIM_TopoIII.
DR PANTHER; PTHR11390; PTHR11390; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF56712; SSF56712; 1.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Reference proteome; Topoisomerase.
FT CHAIN 1..865
FT /note="DNA topoisomerase 3-beta"
FT /id="PRO_0000429773"
FT DOMAIN 6..151
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT REGION 209..214
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 833..865
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 833..849
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 850..865
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 331
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 12
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 116
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 116
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 118
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 73
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 190
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 197
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 333
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT VAR_SEQ 1..64
FT /note="MANLLRVLMVAEKPSIALSIASVLSHGQMSTRRGSTEVHEFDGMFRGFKAHY
FT RVTSVIGHVFSV -> MARCLQGEAVQRCMNLMACFEASKHIIELHLLSVMFS (in
FT isoform 2)"
FT /evidence="ECO:0000303|Ref.3"
FT /id="VSP_055207"
FT CONFLICT 33
FT /note="R -> G (in Ref. 3; BAD95240)"
FT /evidence="ECO:0000305"
FT CONFLICT 83
FT /note="D -> G (in Ref. 3; BAD95240)"
FT /evidence="ECO:0000305"
FT CONFLICT 242
FT /note="Y -> C (in Ref. 3; BAD95240)"
FT /evidence="ECO:0000305"
FT CONFLICT 399
FT /note="D -> V (in Ref. 3; BAD95240)"
FT /evidence="ECO:0000305"
FT CONFLICT 659
FT /note="T -> I (in Ref. 3; BAD95240)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 865 AA; 97021 MW; 1F579AF7C39B8BBA CRC64;
MANLLRVLMV AEKPSIALSI ASVLSHGQMS TRRGSTEVHE FDGMFRGFKA HYRVTSVIGH
VFSVDFPEKY QNWATIDPQD LFDAPIIKKE SNPKAHICRH LSNEARGCSY MVLWLDCDRE
GENICFEVIE STGFDMKDSK RKVYRARFSS VTEKDISKAM DNLVEPNRDE ALAVDARQEI
DLKVGVAFSR FQTSYFQGKY QNLDCRVISY GPCQTPTLGF CVQRYMHINT FKPEKFWALR
PYIRKDGYEL QLEWERRRLF DLEAATVFQK LVVEGRTAKV MDVSEKQEVK GRPAGLNTVN
LLKVASSALG FGPQTAMHLA ERLYTQGFIS YPRTESTAYP SSFDFTDTLR AQVSNPVWGG
YVQRLLSDGF HMPKSGTDAG DHPPITPMRA ATEVMVGGDA WRLYQYVCQH FLGTVSPNCK
YIRTKVELSI GGETFHCTGQ RVTEKGFTAI MPWSAVDEKK LPSFLKGERI EVLRVELYEG
NTAPPDYLTE SELISLMEKH GIGTDASIAV HINNIGERNY VQVQSGRKMV PTALGITLIR
GYQCIDPDLC LPDIRSFIEQ QITLVAKGQA DHSHVVQHVI QQFRRKFSYF VQQIEHMDAL
FEAQFSPLAD SGRALSKCGK CLRYMKHITA VPPRLFCGTC EEVYYLPQKG TVKLYKELTC
PLDNFELVIY SVPGPEGKSF PLCPYCYNSP PFEGIDTLFG ASKTPNAPAK TKTGAGMPCS
LCPHPTCQHS VRNQGVCACP ECEGTLVLDP VSFPKWKLNC NLCSCIVLLP EGAHRITTTS
NRCPECDSAI IEIDFNKKTT PLENGATLHQ GCVLCDELLL SLVEVKHGRS FVRRGGRGRG
RGRGRGRGGR RGSKSVDPKM SFRDF
