TOP3A_ORYSJ
ID TOP3A_ORYSJ Reviewed; 928 AA.
AC C7J0A2; Q8S5U5;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=DNA topoisomerase 3-alpha;
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10131};
GN Name=TOP3A; OrderedLocusNames=Os03g0165000, LOC_Os03g06900;
GN ORFNames=OJ1123F12.5;
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=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 [2]
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 [3]
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 [4]
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: 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 then 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. Essential component of the RMI
CC complex, a complex that plays an important role in the resolution step
CC of homologous recombination, in a process called Holliday Junction
CC dissolution, to limit DNA crossover formation in cells (By similarity).
CC {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; Evidence={ECO:0000250};
CC Note=Binds two Mg(2+) ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Component of the RMI complex, containing at least TOP3A and
CC RMI1. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM15783.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=ABF94145.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC104428; AAM15783.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF94145.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAH92006.1; -; Genomic_DNA.
DR EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_015631257.1; XM_015775771.1.
DR RefSeq; XP_015631258.1; XM_015775772.1.
DR RefSeq; XP_015631259.1; XM_015775773.1.
DR RefSeq; XP_015631260.1; XM_015775774.1.
DR RefSeq; XP_015631261.1; XM_015775775.1.
DR RefSeq; XP_015631262.1; XM_015775776.1.
DR RefSeq; XP_015631263.1; XM_015775777.1.
DR RefSeq; XP_015631265.1; XM_015775779.1.
DR RefSeq; XP_015631266.1; XM_015775780.1.
DR RefSeq; XP_015631267.1; XM_015775781.1.
DR AlphaFoldDB; C7J0A2; -.
DR SMR; C7J0A2; -.
DR STRING; 4530.OS03T0165000-00; -.
DR PRIDE; C7J0A2; -.
DR GeneID; 9269718; -.
DR KEGG; osa:9269718; -.
DR eggNOG; KOG1956; Eukaryota.
DR HOGENOM; CLU_693703_0_0_1; -.
DR InParanoid; C7J0A2; -.
DR OrthoDB; 372111at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; C7J0A2; 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:0008270; F:zinc ion binding; IEA:InterPro.
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 InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR010666; Znf_GRF.
DR PANTHER; PTHR11390; PTHR11390; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF06839; zf-GRF; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SMART; SM00343; ZnF_C2HC; 1.
DR SUPFAM; SSF56712; SSF56712; 1.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW DNA-binding; Isomerase; Magnesium; Metal-binding; Reference proteome;
KW Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..928
FT /note="DNA topoisomerase 3-alpha"
FT /id="PRO_0000429772"
FT DOMAIN 11..157
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT ZN_FING 643..671
FT /note="C4-type"
FT /evidence="ECO:0000255"
FT ZN_FING 806..846
FT /note="GRF-type"
FT ZN_FING 909..925
FT /note="CCHC-type"
FT REGION 222..227
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 389..410
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 741..806
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 849..892
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 862..877
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 344
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 17
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 126
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 126
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 128
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 83
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 198
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 346
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ SEQUENCE 928 AA; 103754 MW; 9BEEF9992C568C0C CRC64;
MHHGGGGGAI RVLNVAEKPS VAKSVAEILS RPSGGMRSRE GRSRYNRVFE FDYSIGGRAC
HMLVTSVTGH LMELEFDDRF RRWHSCDPAD LFHAPVRKSV PQDKQDIKRT LEEEARKCQW
LVLWLDCDRE GENIAYEVID ICAGANSRLN IWRARFSALI DREIHEAVQH LDRPNKLFAD
AVDARQEIDL RIGASFTRFQ TMLLKDAFVL DDTGDDRNII LSYGPCQFPT LGFIVERFWE
IQAHEPEEFW TINCSHTSDE GTASFGWIRG HLFDYSSAVV IYEMCVEEPM ATVQNVRNQE
KLKYPPYPLS TIELQKRASR YFRMSSEHTM KVAEELYQAG FISYPRTETD NFSPNTDLHS
IVHEQVAHPN WGTYAQRLLD PEARLWRNPS NGGHDDKAHP PIHPTKFSAG ETNWTDNHKK
LYELVVRHFL ACCSQPAVGA ETTVEIDIAG EQFNASGRVV LAKNYLDVYR FDSWGGTLLP
TYIIGQQFVP TTLTLDSGMT RPPPLLAEAD LLGCMDKAGI GTDATMHDHI KKLLDRCYAT
KDANTRFSPT NLGEALVMGY DEMGYELWKP YLRSMMEADM KSVSIGTKSK SEVLENCLQQ
MKACFLDARA NKVKLFDAMG TFFARSSRPV NETQNSIETV RPCAACNESE MFLKQRPTGE
FMVGCRGFPQ CRNVVWLPRS LSGAAVTDQV CPTCAPGPVY KIQFKFRRRD IPPNFDVDHL
GCIGGCDDIL KELMELSRFG SHSQTATPAR NQSQTASGVR QGSSRQDLHT SFHPAVQFTN
GQTPVVNPQG FRSTHTQSSG NASGQVQCTS CREPCVLRTA NTEANRGRKF YKCQNLACGF
FAWEDDVENS APRGRGGRGR GGRSSSRQSS ASASAGRRGG TQGRGRRGRG RNADGMMFVA
ATGEPVYGSC FICGDPTHFA NVCPNLGR
