TOP6A_ORYSJ
ID TOP6A_ORYSJ Reviewed; 442 AA.
AC Q0DSV9; A0A0P0VW93; A6P3E1; Q8GZY4;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 2.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Topoisomerase 6 subunit A3;
DE Short=OsTOP6A3;
DE EC=5.6.2.2;
DE AltName: Full=DNA topoisomerase 6 subunit A;
DE Short=OsTOP6A;
DE AltName: Full=Meiotic recombination protein SPO11-3;
DE Short=OsSPO11-3;
DE AltName: Full=OsSPO11C;
GN Name=SPO11-3; Synonyms=TOP6A, TOP6A3;
GN OrderedLocusNames=Os03g0284800, LOC_Os03g17610; ORFNames=OSJNBa0013D02.18;
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 [MRNA].
RC STRAIN=cv. Nipponbare;
RA Yamada K., Kawagishi-Kobayashi M., Shingu Y., Mikawa T., Wakasa K.,
RA Shibata T.;
RT "Isolation and characterization of rice SPO11 genes.";
RL Submitted (JUN-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
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 [4]
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 [5]
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).
CC -!- FUNCTION: Component of the DNA topoisomerase VI involved in chromatin
CC organization and progression of endoreduplication cycles. Relaxes both
CC positive and negative superturns and exhibits a strong decatenase
CC activity (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q57815};
CC -!- SUBUNIT: Homodimer. Heterotetramer of two TOP6A and two TOP6B subunits
CC (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the TOP6A family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAO17008.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=ABF95345.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB219539; BAF65346.1; -; mRNA.
DR EMBL; AC134232; AAO17008.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF95345.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAF11679.2; -; Genomic_DNA.
DR EMBL; AP014959; BAS83614.1; -; Genomic_DNA.
DR RefSeq; XP_015631482.1; XM_015775996.1.
DR AlphaFoldDB; Q0DSV9; -.
DR SMR; Q0DSV9; -.
DR STRING; 4530.OS03T0284800-01; -.
DR PaxDb; Q0DSV9; -.
DR PRIDE; Q0DSV9; -.
DR EnsemblPlants; Os03t0284800-01; Os03t0284800-01; Os03g0284800.
DR Gramene; Os03t0284800-01; Os03t0284800-01; Os03g0284800.
DR KEGG; osa:4332470; -.
DR eggNOG; KOG2795; Eukaryota.
DR HOGENOM; CLU_037229_1_0_1; -.
DR InParanoid; Q0DSV9; -.
DR OMA; NWGEARF; -.
DR OrthoDB; 1272299at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0009330; C:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex; IEA:UniProtKB-UniRule.
DR GO; GO:0000228; C:nuclear chromosome; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IEA:EnsemblPlants.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0042138; P:meiotic DNA double-strand break formation; IBA:GO_Central.
DR GO; GO:0000706; P:meiotic DNA double-strand break processing; IBA:GO_Central.
DR GO; GO:0007131; P:reciprocal meiotic recombination; IBA:GO_Central.
DR CDD; cd00223; TOPRIM_TopoIIB_SPO; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR HAMAP; MF_00132; Top6A; 1.
DR InterPro; IPR002815; Spo11/TopoVI_A.
DR InterPro; IPR013049; Spo11/TopoVI_A_N.
DR InterPro; IPR036078; Spo11/TopoVI_A_sf.
DR InterPro; IPR004085; TopoVI_A.
DR InterPro; IPR034136; TOPRIM_Topo6A/Spo11.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR PANTHER; PTHR10848; PTHR10848; 1.
DR Pfam; PF04406; TP6A_N; 1.
DR PRINTS; PR01550; TOP6AFAMILY.
DR PRINTS; PR01552; TPISMRASE6A.
DR SUPFAM; SSF56726; SSF56726; 1.
PE 2: Evidence at transcript level;
KW DNA-binding; Isomerase; Magnesium; Metal-binding; Nucleotide-binding;
KW Nucleus; Reference proteome; Topoisomerase.
FT CHAIN 1..442
FT /note="Topoisomerase 6 subunit A3"
FT /id="PRO_0000429780"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 185
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:Q9M4A2"
FT BINDING 271
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q57815"
FT BINDING 323
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q57815"
SQ SEQUENCE 442 AA; 48242 MW; 1397867773A726BB CRC64;
MSEKKRRGGA GAGAASGSAS KKPRVSTAAS YAESLRSKLR PDASILATLR SLASACSKSK
PAGSSSSSSS ASKALAAEDD PAASYIVVAD QDSASVTSRI NRLVLAAARS ILSGRGFSFA
VPSRAASNQV YLPDLDRIVL VRRESARPFA NVATARKATI TARVLSLVHA VLRRGIHVTK
RDLFYTDVKL FGDQAQSDAV LDDVSCMLGC TRSSLHVVAS EKGVVVGRLT FADDGDRIDC
TRMGVGGKAI PPNIDRVSGI ESDALFILLV EKDAAFMRLA EDRFYNRFPC IILTAKGQPD
VATRLFLRRL KVELKLPVLA LVDSDPYGLK ILSVYMCGSK NMSYDSANLT TPDIKWLGVR
PSDLDKYRVP EQCRLPMTDH DIKVGKELLE EDFVKQNEGW VKELETMLRT RQKAEIQALS
SFGFQYLTEV YLPLKLQQQD WI
