TOP1A_ARATH
ID TOP1A_ARATH Reviewed; 916 AA.
AC P30181; Q56XA9; Q8RX06;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1993, sequence version 1.
DT 25-MAY-2022, entry version 160.
DE RecName: Full=DNA topoisomerase 1 alpha {ECO:0000305};
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10130};
DE AltName: Full=DNA topoisomerase 1 {ECO:0000303|PubMed:16669064};
DE AltName: Full=DNA topoisomerase I {ECO:0000303|PubMed:16669064};
DE AltName: Full=Protein FASCIATA 5 {ECO:0000305};
DE AltName: Full=Protein MGOUN1 {ECO:0000303|PubMed:20228247};
GN Name=TOP1A {ECO:0000305};
GN Synonyms=FAS5 {ECO:0000305}, MGO1 {ECO:0000303|PubMed:20228247},
GN TOP1 {ECO:0000303|PubMed:16669064},
GN TOP1ALPHA {ECO:0000303|PubMed:12215507};
GN OrderedLocusNames=At5g55300 {ECO:0000312|Araport:AT5G55300};
GN ORFNames=MTE17.1 {ECO:0000312|EMBL:BAB08547.1};
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], AND FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=16669064; DOI=10.1104/pp.99.4.1493;
RA Kieber J.J., Tissier A.F., Signer E.R.;
RT "Cloning and characterization of an Arabidopsis thaliana topoisomerase I
RT gene.";
RL Plant Physiol. 99:1493-1501(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
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).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 403-916.
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 521-916.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12215507; DOI=10.1105/tpc.001925;
RA Takahashi T., Matsuhara S., Abe M., Komeda Y.;
RT "Disruption of a DNA topoisomerase I gene affects morphogenesis in
RT Arabidopsis.";
RL Plant Cell 14:2085-2093(2002).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-170, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [8]
RP SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-170,
RP AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-286, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [10]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=20228247; DOI=10.1105/tpc.109.068296;
RA Graf P., Dolzblasz A., Wuerschum T., Lenhard M., Pfreundt U., Laux T.;
RT "MGOUN1 encodes an Arabidopsis type IB DNA topoisomerase required in stem
RT cell regulation and to maintain developmentally regulated gene silencing.";
RL Plant Cell 22:716-728(2010).
RN [11]
RP FUNCTION.
RX PubMed=25070639; DOI=10.1105/tpc.114.124941;
RA Liu X., Gao L., Dinh T.T., Shi T., Li D., Wang R., Guo L., Xiao L.,
RA Chen X.;
RT "DNA topoisomerase I affects polycomb group protein-mediated epigenetic
RT regulation and plant development by altering nucleosome distribution in
RT Arabidopsis.";
RL Plant Cell 26:2803-2817(2014).
RN [12]
RP INTERACTION WITH DEK3, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=cv. Columbia;
RX PubMed=25387881; DOI=10.1105/tpc.114.129254;
RA Waidmann S., Kusenda B., Mayerhofer J., Mechtler K., Jonak C.;
RT "A DEK domain-containing protein modulates chromatin structure and function
RT in Arabidopsis.";
RL Plant Cell 26:4328-4344(2014).
RN [13]
RP FUNCTION.
RX PubMed=24992598; DOI=10.1371/journal.pgen.1004446;
RA Dinh T.T., Gao L., Liu X., Li D., Li S., Zhao Y., O'Leary M., Le B.,
RA Schmitz R.J., Manavella P.A., Manavella P., Li S., Weigel D., Pontes O.,
RA Ecker J.R., Chen X.;
RT "DNA topoisomerase 1alpha promotes transcriptional silencing of
RT transposable elements through DNA methylation and histone lysine 9
RT dimethylation in Arabidopsis.";
RL PLoS Genet. 10:E1004446-E1004446(2014).
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-(3'-phosphotyrosyl)-
CC enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free
CC DNA strand then rotates around the intact phosphodiester bond on the
CC opposing strand, thus removing DNA supercoils. Finally, in the
CC religation step, the DNA 5'-OH attacks the covalent intermediate to
CC expel the active-site tyrosine and restore the DNA phosphodiester
CC backbone (By similarity). Can complement a TOP1-deficient yeast mutant
CC (PubMed:16669064). Plays a critical role in the maintenance of a
CC regular pattern of organ initiation. Topoisomerases I enzymes (TOP1A
CC and TOP1B) are essential for plant survival (PubMed:12215507).
CC Functions together with the stem cell maintenance gene WUSCHEL (WUS) in
CC stem cell regulation. Required to maintain developmentally regulated
CC gene repression. Functions synergistically with chromatin remodeling
CC factors (PubMed:20228247). Is required for the repression of WUS
CC expression in flower development. Plays a role in polycomb group (PcG)
CC protein-mediated histone H3 trimethylation on 'Lys-27' (H3K27me3) at
CC the WUS gene locus. H3K27me3 induces transcriptional repression of WUS.
CC May assist AGAMOUS (AG) in recruiting PcG proteins to WUS locus.
CC Reduces nucleosome density, especially at genes that are targets of PcG
CC proteins (PubMed:25070639). Plays a role in epigenetic silencing.
CC Involved in RNA-directed DNA methylation (RdDM) by promoting Pol V
CC transcription to generate long non-coding RNA transcripts. Is
CC dispensable for Pol IV-mediated small interfering RNA (siRNA)
CC biogenesis. Promotes transposable element (TE) silencing at endogenous
CC RdDM target loci through histone H3 dimethylation of 'Lys-9' (H3K9me2).
CC Promotes the production of Pol V-dependent long non-coding transcripts
CC that facilitate the recruitment of siRNA-AGO4 and AGO4 occupancy at TEs
CC (PubMed:24992598). {ECO:0000250|UniProtKB:P11387,
CC ECO:0000269|PubMed:12215507, ECO:0000269|PubMed:16669064,
CC ECO:0000269|PubMed:20228247, ECO:0000269|PubMed:24992598,
CC ECO:0000269|PubMed:25070639}.
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:PRU10130};
CC -!- SUBUNIT: Interacts with DEK3. {ECO:0000269|PubMed:25387881}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19245862}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=P30181-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in inflorescence meristems. Expressed in
CC primordia of sepals, petals, stamens, carpels and ovules. Expressed in
CC midstage embryos. {ECO:0000269|PubMed:20228247}.
CC -!- DISRUPTION PHENOTYPE: Defects in phyllotaxis and plant architecture.
CC Morphological abnormalities of several organs (PubMed:12215507).
CC Defects in cellular development and organization of both the shoot and
CC the root meristem (PubMed:20228247). {ECO:0000269|PubMed:12215507,
CC ECO:0000269|PubMed:20228247}.
CC -!- MISCELLANEOUS: Eukaryotic topoisomerase I and II can relax both
CC negative and positive supercoils, whereas prokaryotic enzymes relax
CC only negative supercoils.
CC -!- SIMILARITY: Belongs to the type IB topoisomerase family. {ECO:0000305}.
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DR EMBL; X57544; CAA40763.1; -; mRNA.
DR EMBL; AB015479; BAB08547.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96612.1; -; Genomic_DNA.
DR EMBL; AY090993; AAM14018.1; -; mRNA.
DR EMBL; AK221766; BAD93853.1; -; mRNA.
DR PIR; S22864; S22864.
DR RefSeq; NP_200341.1; NM_124912.5. [P30181-1]
DR AlphaFoldDB; P30181; -.
DR SMR; P30181; -.
DR BioGRID; 20867; 4.
DR IntAct; P30181; 3.
DR STRING; 3702.AT5G55300.2; -.
DR iPTMnet; P30181; -.
DR PaxDb; P30181; -.
DR PRIDE; P30181; -.
DR EnsemblPlants; AT5G55300.1; AT5G55300.1; AT5G55300. [P30181-1]
DR GeneID; 835623; -.
DR Gramene; AT5G55300.1; AT5G55300.1; AT5G55300. [P30181-1]
DR KEGG; ath:AT5G55300; -.
DR Araport; AT5G55300; -.
DR eggNOG; KOG0981; Eukaryota.
DR HOGENOM; CLU_009193_1_2_1; -.
DR InParanoid; P30181; -.
DR OMA; CKSECED; -.
DR PhylomeDB; P30181; -.
DR BRENDA; 5.6.2.1; 399.
DR BRENDA; 5.99.1.2; 399.
DR PRO; PR:P30181; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P30181; baseline and differential.
DR Genevisible; P30181; AT.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IBA:GO_Central.
DR GO; GO:0007059; P:chromosome segregation; IBA:GO_Central.
DR GO; GO:0006260; P:DNA replication; IBA:GO_Central.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR CDD; cd00659; Topo_IB_C; 1.
DR Gene3D; 1.10.10.41; -; 1.
DR Gene3D; 1.10.132.10; -; 1.
DR Gene3D; 2.170.11.10; -; 1.
DR Gene3D; 3.90.15.10; -; 1.
DR InterPro; IPR011010; DNA_brk_join_enz.
DR InterPro; IPR013034; DNA_topo_DNA_db_N_dom1.
DR InterPro; IPR013030; DNA_topo_DNA_db_N_dom2.
DR InterPro; IPR001631; TopoI.
DR InterPro; IPR018521; TopoI_AS.
DR InterPro; IPR025834; TopoI_C_dom.
DR InterPro; IPR014711; TopoI_cat_a-hlx-sub_euk.
DR InterPro; IPR014727; TopoI_cat_a/b-sub_euk.
DR InterPro; IPR013500; TopoI_cat_euk.
DR InterPro; IPR008336; TopoI_DNA-bd_euk.
DR InterPro; IPR036202; TopoI_DNA-bd_euk_N_sf.
DR InterPro; IPR013499; TopoI_euk.
DR Pfam; PF14370; Topo_C_assoc; 1.
DR Pfam; PF01028; Topoisom_I; 1.
DR Pfam; PF02919; Topoisom_I_N; 1.
DR PRINTS; PR00416; EUTPISMRASEI.
DR SMART; SM00435; TOPEUc; 1.
DR SUPFAM; SSF56349; SSF56349; 1.
DR SUPFAM; SSF56741; SSF56741; 1.
DR PROSITE; PS00176; TOPOISOMERASE_I_EUK; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Coiled coil; DNA-binding; Isomerase; Nucleus;
KW Phosphoprotein; Reference proteome; Topoisomerase.
FT CHAIN 1..916
FT /note="DNA topoisomerase 1 alpha"
FT /id="PRO_0000145206"
FT REGION 1..369
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 577..578
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT REGION 640..645
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT REGION 731..733
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT COILED 778..860
FT /evidence="ECO:0000255"
FT COMPBIAS 28..106
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 107..127
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 128..152
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 153..179
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 188..216
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 230..253
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 254..284
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 300..329
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 354..369
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 872
FT /note="O-(3'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10130"
FT SITE 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 514
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 563
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 595
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 652
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 678
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 720
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 777
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT SITE 795
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P11387"
FT MOD_RES 170
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19245862"
FT MOD_RES 286
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19376835"
SQ SEQUENCE 916 AA; 102799 MW; 84BF47913F14454F CRC64;
MGTETVSKPV MDNGSGDSDD DKPLAFKRNN TVASNSNQSK SNSQRSKAVP TTKVSPMRSP
VTSPNGTTPS NKTSIVKSSM PSSSSKASPA KSPLRNDMPS TVKDRSQLQK DQSECKIEHE
DSEDDRPLSS ILSGNKGPTS SRQVSSPQPE KKNNGDRPLD RASRIIKDES DDETPISSMF
RKKIDSGMSG GNQLSNDEKK PLVQKLHQNG STVKNEVPNG KVLGKRPLEK NSSADQSSLK
KAKISASPTS VKMKQDSVKK EIDDKGRVLV SPKMKAKQLS TREDGTDDDD DDDVPISKRF
KSDSSNSNTS SAKPKAVKLN STSSAAKPKA RNVVSPRSRA MTKNTKKVTK DSKYSTSSKS
SPSSGDGQKK WTTLVHNGVI FPPPYKPHGI KILYKGKPVD LTIEQEEVAT MFAVMRETDY
YTKPQFRENF WNDWRRLLGK KHVIQKLDDC DFTPIYEWHL EEKEKKKQMS TEEKKALKEE
KMKQEEKYMW AVVDGVKEKI GNFRVEPPGL FRGRGEHPKM GKLKKRIHPC EITLNIGKGA
PIPECPIAGE RWKEVKHDNT VTWLAFWADP INPKEFKYVF LGAGSSLKGL SDKEKYEKAR
NLTDHIDNIR TTYTKNFTAK DVKMRQIAVA TYLIDKLALR AGNEKDDDEA DTVGCCTLKV
GNVECIPPNK IKFDFLGKDS IQYVNTVEVE PLVYKAIGQF QAGKSKTDDL FDELDTSKLN
AHLKELVPGL TAKVFRTYNA SITLDEMLSQ ETKDGDVTQK IVVYQKANKE VAIICNHQRT
VSKTHGAQIE KLTARIEELK EVLKELKTNL DRAKKGKPPL EGSDGKKIRS LEPNAWEKKI
AQQSAKIEKM ERDMHTKEDL KTVALGTSKI NYLDPRITVA WCKRHEVPIE KIFTKSLLEK
FAWAMDVEPE YRFSRR
