ID   SPO14_ORYSJ             Reviewed;         487 AA.
AC   Q2QM00; A0A0P0YD99; D2K3B6;
DT   09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT   11-JUL-2006, sequence version 2.
DT   03-AUG-2022, entry version 114.
DE   RecName: Full=Meiotic recombination protein SPO11-4;
DE            Short=OsSPO11-4;
DE   AltName: Full=OsSPO11D;
GN   Name=SPO11-4; OrderedLocusNames=Os12g0622500, LOC_Os12g42760;
GN   ORFNames=OsJ_36918;
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], FUNCTION, COFACTOR, HOMODIMERIZATION, AND
RP   INTERACTION WITH TOP6B.
RC   STRAIN=cv. Zhonghua 10;
RX   PubMed=21637817; DOI=10.1371/journal.pone.0020327;
RA   An X.J., Deng Z.Y., Wang T.;
RT   "OsSpo11-4, a rice homologue of the archaeal TopVIA protein, mediates
RT   double-strand DNA cleavage and interacts with OsTopVIB.";
RL   PLoS ONE 6:E20327-E20327(2011).
RN   [2]
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   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
RN   [4]
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   [5]
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   [6]
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   [7]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [8]
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: Required for meiotic recombination. Mediates DNA cleavage
CC       that forms the double-strand breaks (DSB) that initiate meiotic
CC       recombination. Possesses double-stranded DNA cleavage activity in
CC       vitro. {ECO:0000269|PubMed:21637817}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:21637817};
CC   -!- SUBUNIT: Homodimer. Interacts with TOP6B.
CC       {ECO:0000269|PubMed:21637817}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- MISCELLANEOUS: Plants silencing TPO6A1 are sterile due to defect in
CC       male meiosis. {ECO:0000305|PubMed:21637817}.
CC   -!- SIMILARITY: Belongs to the TOP6A family. {ECO:0000305}.
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DR   EMBL; GU177866; ACZ58078.2; -; mRNA.
DR   EMBL; AB219540; BAF65347.1; -; mRNA.
DR   EMBL; DP000011; ABA99412.2; -; Genomic_DNA.
DR   EMBL; AP008218; BAF30326.1; -; Genomic_DNA.
DR   EMBL; AP014968; BAT18151.1; -; Genomic_DNA.
DR   EMBL; CM000149; EAZ21266.1; -; Genomic_DNA.
DR   EMBL; AK101363; BAG95027.1; -; mRNA.
DR   RefSeq; XP_015618337.1; XM_015762851.1.
DR   AlphaFoldDB; Q2QM00; -.
DR   SMR; Q2QM00; -.
DR   STRING; 4530.OS12T0622500-01; -.
DR   PaxDb; Q2QM00; -.
DR   PRIDE; Q2QM00; -.
DR   EnsemblPlants; Os12t0622500-01; Os12t0622500-01; Os12g0622500.
DR   GeneID; 4352826; -.
DR   Gramene; Os12t0622500-01; Os12t0622500-01; Os12g0622500.
DR   KEGG; osa:4352826; -.
DR   eggNOG; KOG2795; Eukaryota.
DR   HOGENOM; CLU_560677_0_0_1; -.
DR   InParanoid; Q2QM00; -.
DR   OMA; GAICENA; -.
DR   OrthoDB; 1272299at2759; -.
DR   Proteomes; UP000000763; Chromosome 12.
DR   Proteomes; UP000007752; Chromosome 12.
DR   Proteomes; UP000059680; Chromosome 12.
DR   Genevisible; Q2QM00; OS.
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:InterPro.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
DR   GO; GO:0030957; F:Tat protein binding; IPI:UniProtKB.
DR   GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR   GO; GO:0006302; P:double-strand break repair; IMP:UniProtKB.
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; IMP:UniProtKB.
DR   CDD; cd00223; TOPRIM_TopoIIB_SPO; 1.
DR   Gene3D; 1.10.10.10; -; 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   1: Evidence at protein level;
KW   Hydrolase; Magnesium; Metal-binding; Nucleus; Reference proteome.
FT   CHAIN           1..487
FT                   /note="Meiotic recombination protein SPO11-4"
FT                   /id="PRO_0000429779"
FT   REGION          1..56
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..21
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        213
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q9M4A2"
FT   BINDING         301
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q57815"
FT   BINDING         353
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q57815"
FT   CONFLICT        7
FT                   /note="D -> G (in Ref. 1; ACZ58078)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   487 AA;  55342 MW;  72D84ACBD29F3EC7 CRC64;
     MDDSTDDDSY HPRKHYAYDR QVSSSRWRTS REYIRGPGPE THTTESAQDG QDPPAGVYSY
     GYFSGSGNDP QVQGHFVPEI QKYNPYVIFK GEQLPVPIWE LPEEKVQDFH DRYFIAKDKS
     RVEARKTLNR LLEGNINTIE RGHGYKFNIP KYTDNMEFNE EVKVSLAKAG KTISRSFCNA
     NQREVASRTG YTIDLIERTL GAGLNISKRT VLYTNKDLFG DQSKSDQAIN DICALTNIRR
     GSLGIIAAEK GIVVGNIFLE LTNGKSISCS IGVQIPHRLD QIKDVCVEIG SRNIEYILVV
     EKHTMLNYLL EMDYHTNNNC IILTGCGMPT LQTRDFLRFL KQRTGLPVFG LCDPDPEGIS
     ILATYARGSC NSAYDNFNIS VPSICWVGLS SSDMIKLNLS ETNYSRLSRE DKTMLKNLWQ
     DDLSDVWKRR IEEMISFDKK ASFEAIHSLG FDYFATNLLP DMINKVREGY VQVQEKKEPQ
     DTEASED