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Protein

DNA topoisomerase 1 alpha

Gene

TOP1A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then rotates around the intact phosphodiester bond on the opposing strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Can complement a TOP1-deficient yeast mutant (PubMed:16669064). Plays a critical role in the maintenance of a regular pattern of organ initiation. Topoisomerases I enzymes (TOP1A and TOP1B) are essential for plant survival (PubMed:12215507). Functions together with the stem cell maintenance gene WUSCHEL (WUS) in stem cell regulation. Required to maintain developmentally regulated gene repression. Functions synergistically with chromatin remodeling factors (PubMed:20228247). Is required for the repression of WUS expression in flower development. Plays a role in polycomb group (PcG) protein-mediated histone H3 trimethylation on 'Lys-27' (H3K27me3) at the WUS gene locus. H3K27me3 induces transcriptional repression of WUS. May assist AGAMOUS (AG) in recruiting PcG proteins to WUS locus. Reduces nucleosome density, especially at genes that are targets of PcG proteins (PubMed:25070639). Plays a role in epigenetic silencing. Involved in RNA-directed DNA methylation (RdDM) by promoting Pol V transcription to generate long non-coding RNA transcripts. Is dispensable for Pol IV-mediated small interfering RNA (siRNA) biogenesis. Promotes transposable element (TE) silencing at endogenous RdDM target loci through histone H3 dimethylation of 'Lys-9' (H3K9me2). Promotes the production of Pol V-dependent long non-coding transcripts that facilitate the recruitment of siRNA-AGO4 and AGO4 occupancy at TEs (PubMed:24992598).By similarity5 Publications

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei872O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BRENDAi5.99.1.2. 399.
ReactomeiR-ATH-4615885. SUMOylation of DNA replication proteins.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 alphaCurated (EC:5.99.1.2PROSITE-ProRule annotation)
Alternative name(s):
DNA topoisomerase 11 Publication
DNA topoisomerase I1 Publication
Protein FASCIATA 5Curated
Protein MGOUN11 Publication
Gene namesi
Name:TOP1ACurated
Synonyms:FAS5Curated, MGO11 Publication, TOP11 Publication, TOP1ALPHA1 Publication
Ordered Locus Names:At5g55300Imported
ORF Names:MTE17.1
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G55300.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Defects in phyllotaxis and plant architecture. Morphological abnormalities of several organs (PubMed:12215507). Defects in cellular development and organization of both the shoot and the root meristem (PubMed:20228247).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001452061 – 916DNA topoisomerase 1 alphaAdd BLAST916

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei170PhosphoserineCombined sources1
Modified residuei286PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP30181.

PTM databases

iPTMnetiP30181.

Expressioni

Tissue specificityi

Expressed in inflorescence meristems. Expressed in primordia of sepals, petals, stamens, carpels and ovules. Expressed in midstage embryos.1 Publication

Gene expression databases

ExpressionAtlasiP30181. baseline and differential.
GenevisibleiP30181. AT.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei466Interaction with DNABy similarity1
Sitei514Interaction with DNABy similarity1
Sitei563Interaction with DNABy similarity1
Sitei595Interaction with DNABy similarity1
Sitei652Interaction with DNABy similarity1
Sitei678Interaction with DNABy similarity1
Sitei720Interaction with DNABy similarity1
Sitei777Interaction with DNABy similarity1
Sitei795Interaction with DNABy similarity1

Protein-protein interaction databases

BioGridi20867. 3 interactors.
IntActiP30181. 2 interactors.
STRINGi3702.AT5G55300.2.

Structurei

3D structure databases

ProteinModelPortaliP30181.
SMRiP30181.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni577 – 578Interaction with DNABy similarity2
Regioni640 – 645Interaction with DNABy similarity6
Regioni731 – 733Interaction with DNABy similarity3

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili778 – 860Sequence analysisAdd BLAST83

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi34 – 146Ser-richPROSITE-ProRule annotationAdd BLAST113
Compositional biasi284 – 293Asp-richPROSITE-ProRule annotation10

Sequence similaritiesi

Belongs to the type IB topoisomerase family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG0981. Eukaryota.
COG3569. LUCA.
HOGENOMiHOG000105469.
InParanoidiP30181.
KOiK03163.
PhylomeDBiP30181.

Family and domain databases

CDDicd00659. Topo_IB_C. 1 hit.
Gene3Di1.10.10.41. 1 hit.
1.10.132.10. 1 hit.
2.170.11.10. 2 hits.
3.90.15.10. 1 hit.
InterProiIPR011010. DNA_brk_join_enz.
IPR013034. DNA_topo_domain1.
IPR001631. TopoI.
IPR018521. TopoI_AS.
IPR025834. TopoI_C_dom.
IPR014711. TopoI_cat_a-hlx-sub_euk.
IPR014727. TopoI_cat_a/b-sub_euk.
IPR013500. TopoI_cat_euk.
IPR008336. TopoI_DNA-bd_euk.
IPR013030. TopoI_DNA-bd_mixed-a/b_euk.
IPR013499. TopoI_euk.
[Graphical view]
PfamiPF14370. Topo_C_assoc. 1 hit.
PF01028. Topoisom_I. 1 hit.
PF02919. Topoisom_I_N. 1 hit.
[Graphical view]
PRINTSiPR00416. EUTPISMRASEI.
SMARTiSM00435. TOPEUc. 1 hit.
[Graphical view]
SUPFAMiSSF56349. SSF56349. 2 hits.
SSF56741. SSF56741. 1 hit.
PROSITEiPS00176. TOPOISOMERASE_I_EUK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: P30181-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGTETVSKPV MDNGSGDSDD DKPLAFKRNN TVASNSNQSK SNSQRSKAVP
60 70 80 90 100
TTKVSPMRSP VTSPNGTTPS NKTSIVKSSM PSSSSKASPA KSPLRNDMPS
110 120 130 140 150
TVKDRSQLQK DQSECKIEHE DSEDDRPLSS ILSGNKGPTS SRQVSSPQPE
160 170 180 190 200
KKNNGDRPLD RASRIIKDES DDETPISSMF RKKIDSGMSG GNQLSNDEKK
210 220 230 240 250
PLVQKLHQNG STVKNEVPNG KVLGKRPLEK NSSADQSSLK KAKISASPTS
260 270 280 290 300
VKMKQDSVKK EIDDKGRVLV SPKMKAKQLS TREDGTDDDD DDDVPISKRF
310 320 330 340 350
KSDSSNSNTS SAKPKAVKLN STSSAAKPKA RNVVSPRSRA MTKNTKKVTK
360 370 380 390 400
DSKYSTSSKS SPSSGDGQKK WTTLVHNGVI FPPPYKPHGI KILYKGKPVD
410 420 430 440 450
LTIEQEEVAT MFAVMRETDY YTKPQFRENF WNDWRRLLGK KHVIQKLDDC
460 470 480 490 500
DFTPIYEWHL EEKEKKKQMS TEEKKALKEE KMKQEEKYMW AVVDGVKEKI
510 520 530 540 550
GNFRVEPPGL FRGRGEHPKM GKLKKRIHPC EITLNIGKGA PIPECPIAGE
560 570 580 590 600
RWKEVKHDNT VTWLAFWADP INPKEFKYVF LGAGSSLKGL SDKEKYEKAR
610 620 630 640 650
NLTDHIDNIR TTYTKNFTAK DVKMRQIAVA TYLIDKLALR AGNEKDDDEA
660 670 680 690 700
DTVGCCTLKV GNVECIPPNK IKFDFLGKDS IQYVNTVEVE PLVYKAIGQF
710 720 730 740 750
QAGKSKTDDL FDELDTSKLN AHLKELVPGL TAKVFRTYNA SITLDEMLSQ
760 770 780 790 800
ETKDGDVTQK IVVYQKANKE VAIICNHQRT VSKTHGAQIE KLTARIEELK
810 820 830 840 850
EVLKELKTNL DRAKKGKPPL EGSDGKKIRS LEPNAWEKKI AQQSAKIEKM
860 870 880 890 900
ERDMHTKEDL KTVALGTSKI NYLDPRITVA WCKRHEVPIE KIFTKSLLEK
910
FAWAMDVEPE YRFSRR
Length:916
Mass (Da):102,799
Last modified:April 1, 1993 - v1
Checksum:i84BF47913F14454F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X57544 mRNA. Translation: CAA40763.1.
AB015479 Genomic DNA. Translation: BAB08547.1.
CP002688 Genomic DNA. Translation: AED96612.1.
AY090993 mRNA. Translation: AAM14018.1.
AK221766 mRNA. Translation: BAD93853.1.
PIRiS22864.
RefSeqiNP_200341.1. NM_124912.5. [P30181-1]
UniGeneiAt.197.

Genome annotation databases

EnsemblPlantsiAT5G55300.1; AT5G55300.1; AT5G55300. [P30181-1]
GeneIDi835623.
GrameneiAT5G55300.1; AT5G55300.1; AT5G55300.
KEGGiath:AT5G55300.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X57544 mRNA. Translation: CAA40763.1.
AB015479 Genomic DNA. Translation: BAB08547.1.
CP002688 Genomic DNA. Translation: AED96612.1.
AY090993 mRNA. Translation: AAM14018.1.
AK221766 mRNA. Translation: BAD93853.1.
PIRiS22864.
RefSeqiNP_200341.1. NM_124912.5. [P30181-1]
UniGeneiAt.197.

3D structure databases

ProteinModelPortaliP30181.
SMRiP30181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi20867. 3 interactors.
IntActiP30181. 2 interactors.
STRINGi3702.AT5G55300.2.

PTM databases

iPTMnetiP30181.

Proteomic databases

PaxDbiP30181.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G55300.1; AT5G55300.1; AT5G55300. [P30181-1]
GeneIDi835623.
GrameneiAT5G55300.1; AT5G55300.1; AT5G55300.
KEGGiath:AT5G55300.

Organism-specific databases

TAIRiAT5G55300.

Phylogenomic databases

eggNOGiKOG0981. Eukaryota.
COG3569. LUCA.
HOGENOMiHOG000105469.
InParanoidiP30181.
KOiK03163.
PhylomeDBiP30181.

Enzyme and pathway databases

BRENDAi5.99.1.2. 399.
ReactomeiR-ATH-4615885. SUMOylation of DNA replication proteins.

Miscellaneous databases

PROiP30181.

Gene expression databases

ExpressionAtlasiP30181. baseline and differential.
GenevisibleiP30181. AT.

Family and domain databases

CDDicd00659. Topo_IB_C. 1 hit.
Gene3Di1.10.10.41. 1 hit.
1.10.132.10. 1 hit.
2.170.11.10. 2 hits.
3.90.15.10. 1 hit.
InterProiIPR011010. DNA_brk_join_enz.
IPR013034. DNA_topo_domain1.
IPR001631. TopoI.
IPR018521. TopoI_AS.
IPR025834. TopoI_C_dom.
IPR014711. TopoI_cat_a-hlx-sub_euk.
IPR014727. TopoI_cat_a/b-sub_euk.
IPR013500. TopoI_cat_euk.
IPR008336. TopoI_DNA-bd_euk.
IPR013030. TopoI_DNA-bd_mixed-a/b_euk.
IPR013499. TopoI_euk.
[Graphical view]
PfamiPF14370. Topo_C_assoc. 1 hit.
PF01028. Topoisom_I. 1 hit.
PF02919. Topoisom_I_N. 1 hit.
[Graphical view]
PRINTSiPR00416. EUTPISMRASEI.
SMARTiSM00435. TOPEUc. 1 hit.
[Graphical view]
SUPFAMiSSF56349. SSF56349. 2 hits.
SSF56741. SSF56741. 1 hit.
PROSITEiPS00176. TOPOISOMERASE_I_EUK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTOP1A_ARATH
AccessioniPrimary (citable) accession number: P30181
Secondary accession number(s): Q56XA9, Q8RX06
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: November 30, 2016
This is version 127 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.