TOP3A_ARATH
ID TOP3A_ARATH Reviewed; 926 AA.
AC Q9LVP1;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=DNA topoisomerase 3-alpha;
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10131};
GN Name=TOP3A; OrderedLocusNames=At5g63920; ORFNames=MGI19.16;
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 [MRNA], FUNCTION, INTERACTION WITH RIM1, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19096507; DOI=10.1371/journal.pgen.1000285;
RA Hartung F., Suer S., Knoll A., Wurz-Wildersinn R., Puchta H.;
RT "Topoisomerase 3alpha and RMI1 suppress somatic crossovers and are
RT essential for resolution of meiotic recombination intermediates in
RT Arabidopsis thaliana.";
RL PLoS Genet. 4:E1000285-E1000285(2008).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [3]
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).
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. Together with
CC RMI1, is essential for the resolution of meiotic recombination
CC intermediates, a step that prevents entanglement of the parental
CC chromosomes. May have DNA decatenation activity.
CC {ECO:0000269|PubMed:19096507}.
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. The RMI complex interacts with RECQL4A (By similarity).
CC {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Severe developmental defects and early lethality.
CC {ECO:0000269|PubMed:19096507}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. {ECO:0000305}.
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DR EMBL; EU295446; ACA50279.1; -; mRNA.
DR EMBL; AB019227; BAA96895.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97816.1; -; Genomic_DNA.
DR RefSeq; NP_201197.1; NM_125788.7.
DR AlphaFoldDB; Q9LVP1; -.
DR SMR; Q9LVP1; -.
DR STRING; 3702.AT5G63920.1; -.
DR iPTMnet; Q9LVP1; -.
DR PaxDb; Q9LVP1; -.
DR PRIDE; Q9LVP1; -.
DR ProteomicsDB; 234335; -.
DR EnsemblPlants; AT5G63920.1; AT5G63920.1; AT5G63920.
DR GeneID; 836513; -.
DR Gramene; AT5G63920.1; AT5G63920.1; AT5G63920.
DR KEGG; ath:AT5G63920; -.
DR Araport; AT5G63920; -.
DR TAIR; locus:2160841; AT5G63920.
DR eggNOG; KOG1956; Eukaryota.
DR HOGENOM; CLU_002929_1_2_1; -.
DR InParanoid; Q9LVP1; -.
DR OMA; EHICFEV; -.
DR OrthoDB; 373433at2759; -.
DR PhylomeDB; Q9LVP1; -.
DR PRO; PR:Q9LVP1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LVP1; baseline and differential.
DR Genevisible; Q9LVP1; AT.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
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:0007059; P:chromosome segregation; IMP:TAIR.
DR GO; GO:0006281; P:DNA repair; IMP:TAIR.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR GO; GO:0051321; P:meiotic cell cycle; IMP:TAIR.
DR GO; GO:0000278; P:mitotic cell cycle; IMP:TAIR.
DR GO; GO:0000712; P:resolution of meiotic recombination intermediates; IMP:TAIR.
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; IPR013498; Topo_IA_Znf.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034144; TOPRIM_TopoIII.
DR InterPro; IPR001878; Znf_CCHC.
DR InterPro; IPR036875; Znf_CCHC_sf.
DR InterPro; IPR010666; Znf_GRF.
DR PANTHER; PTHR11390; PTHR11390; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF01396; zf-C4_Topoisom; 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; 2.
DR SUPFAM; SSF56712; SSF56712; 1.
DR SUPFAM; SSF57756; SSF57756; 2.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
DR PROSITE; PS50158; ZF_CCHC; 2.
PE 1: Evidence at protein level;
KW DNA-binding; Isomerase; Magnesium; Meiosis; Metal-binding;
KW Reference proteome; Repeat; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..926
FT /note="DNA topoisomerase 3-alpha"
FT /id="PRO_0000429771"
FT DOMAIN 10..154
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT ZN_FING 642..670
FT /note="C4-type"
FT /evidence="ECO:0000255"
FT ZN_FING 767..782
FT /note="CCHC-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT ZN_FING 805..844
FT /note="GRF-type"
FT ZN_FING 901..917
FT /note="CCHC-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00047"
FT REGION 219..224
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 740..760
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 775..806
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 849..890
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 849..863
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 342
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 16
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 123
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 123
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 125
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 80
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 202
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 344
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
SQ SEQUENCE 926 AA; 103407 MW; 806A59EAD08CBB08 CRC64;
MSRRGGGPVT VLNVAEKPSV AKSVAGILSR GTFRTREGRS RYNKIFEFDY AINGQPCRML
MTSVIGHLME LEFADRYRKW HSCDPADLYQ APVMKHVPED KKDIKKTLEE EARKSDWLVL
WLDCDREGEN IAFEVVDVCR AVKHNLFIRR AHFSALIDRD IHEAVQNLRD PNQLFAEAVD
ARQEIDLRIG ASFTRFQTML LRDRFAIDST GEERSRVISY GPCQFPTLGF IVERYWEIQA
HEPEEFWTIN CSHQSEEGLA TFNWMRGHLF DYASAVILYE MCVEEPTATV MNVPHPRERF
KYPPYPLNTI ELEKRASRYF RLSSEHTMKV AEELYQAGFI SYPRTETDSF SSRTDLRAMV
EEQTRHPAWG SYAQRLLEPE GGLWRNPANG GHDDKAHPPI HPTKFSSGES NWSRDHLNVY
ELVVRHYLAC VSQPAVAAET TVEIDIAGER FSASGRAILA KNYLEVYRFE SWGGSVIPVY
EKGQQFIPTT LTLDAAVTRP PPLLCEADLL SCMDKAGIGT DATMHDHIKK LLDRGYATKD
ANTRFSPTNL GEALVMGYDD MGYELWKPNL RALMEHDMNE VSVGRKTKAE VLETCLQQMK
ACFLDARVKK SKLLEAMTIF FERSNNTDES ESQTAGEVVR RCNLCNESDM ALRKNRDGNF
MVGCMNYPQC RNAVWLPGPT LEASVTTNVC QSCGPGPVYK ILFKFRQIGI PPGFDVNHLG
CVGGCDDILK QLIDICGTGS RSQARRTPGT APSNNIQGSN TRQSNVCIHC QQRGHASTNC
PSRVPASRNS RPTATNPRND ESTVSCNTCG SQCVLRTANT EANRGRQFFS CPTQGCSFFA
WEDSINNSSG NATTGSNSGG SGRRGSRGRG RGGRGGQSSG GRRGSGTSFV SATGEPVSGI
RCFSCGDPSH FANACPNRNN SNGNYF
