TOP3B_ORYSJ
ID TOP3B_ORYSJ Reviewed; 866 AA.
AC Q0J0S6; A0A0P0XQ49;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=DNA topoisomerase 3-beta;
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10131};
GN Name=TOP3B; OrderedLocusNames=Os09g0500600, LOC_Os09g32450;
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=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 [2]
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 [3]
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 [4]
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: 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 -!- SIMILARITY: Belongs to the type IA topoisomerase family. {ECO:0000305}.
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DR EMBL; AP008215; BAF25492.1; -; Genomic_DNA.
DR EMBL; AP014965; BAT08809.1; -; Genomic_DNA.
DR EMBL; AK066999; BAG90220.1; -; mRNA.
DR RefSeq; XP_015612275.1; XM_015756789.1.
DR AlphaFoldDB; Q0J0S6; -.
DR SMR; Q0J0S6; -.
DR STRING; 4530.OS09T0500600-01; -.
DR PaxDb; Q0J0S6; -.
DR PRIDE; Q0J0S6; -.
DR EnsemblPlants; Os09t0500600-01; Os09t0500600-01; Os09g0500600.
DR GeneID; 4347482; -.
DR Gramene; Os09t0500600-01; Os09t0500600-01; Os09g0500600.
DR KEGG; osa:4347482; -.
DR eggNOG; KOG1957; Eukaryota.
DR HOGENOM; CLU_002929_1_0_1; -.
DR InParanoid; Q0J0S6; -.
DR OMA; TYPRVDT; -.
DR OrthoDB; 373433at2759; -.
DR Proteomes; UP000000763; Chromosome 9.
DR Proteomes; UP000059680; Chromosome 9.
DR Genevisible; Q0J0S6; OS.
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: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 DNA-binding; Isomerase; Magnesium; Metal-binding; Reference proteome;
KW Topoisomerase.
FT CHAIN 1..866
FT /note="DNA topoisomerase 3-beta"
FT /id="PRO_0000429774"
FT DOMAIN 4..149
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT REGION 207..212
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 830..866
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 830..849
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 850..866
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 329
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 10
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 114
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 114
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
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 SITE 71
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 188
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 195
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 331
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ SEQUENCE 866 AA; 96832 MW; 6DD49047FA9F1149 CRC64;
MAPTVLMVAE KPSIALSIAS ALSGGRMSTR KGSTDVHEFD GMFQGSHAFF KVTSVIGHVL
SVDFPPAYQN WEGTDPMDLF VAPVLRSECN PKAHIRRHLA QEARGCTYLV LWLDCDREGE
NICYEVIDCT GIPKSEVGRR IFRAKFSSVT EKDIMDAMNN LVLPSKDEAL AVDARQEIDL
KVGVAFTRFQ TRYFQGKYGN LDSRVISYGP CQTPTLGFCV QRYQQITTFK PEKFWSLKTY
VIKDGNEIQL EWDRKKLFDF DVTVMFQKMV ASDGILKVTD ISVKEECKAR PPGLNTVNLL
KVASSALGIG PQTAMHLAER LYTQGFISYP RTESTAYPSS FDFRSALAAL AHNPLWSNDV
RTLLDTGFVK PKQGHDAGDH PPITPMRLAT EEALGTDAWR LYQYICQHFI GTVSPDCRYT
RTSIEFTSGG ETFHCVGNRV TSKGFTSIMP WLAVSENNIP AYKKGDAVSI HKVDIYEGST
TPPDYLSESE LISLMEKNGI GTDASIPVHV NNICERNYVQ VNSGRRLVPT PLGTTLIRGY
QCIDADLCLP DIRRFIEQQI TLIAKGEADH LQVVQHVLQQ FMKKYSYFVK KIENMDALFE
AQFSPLADSG RLLSKCGKCA RYMKYISTQP MRLYCVTCEE VYYLPQNGSI KLYKEIICPL
DGFELLLFSM VGPDAKSFPL CPFCYNSPPF EGIDKLFGAL KLDDTGKVGK GAGMPCFLCL
HPTCKQSMIT QGVCACPECT GTLILDPVSA PKWRLYCNRC NCIVLLPHAA HKISTTDKKC
PTCESTIIEV DFNKKTTPLK DGATLHEGCI LCDELLHSLI EMKHGKSFFM RRGRGRGRGR
GRGRGSSRGR RGSSRHDDPK MSFRDF
