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Protein

DNA topoisomerase 1

Gene

TOP1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 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 undergoes passage around the unbroken 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).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei514 – 5141Interaction with DNABy similarity
Sitei563 – 5631Interaction with DNABy similarity
Sitei595 – 5951Interaction with DNABy similarity
Sitei652 – 6521Interaction with DNABy similarity
Sitei678 – 6781Interaction with DNABy similarity
Sitei720 – 7201Interaction with DNABy similarity
Sitei777 – 7771Interaction with DNABy similarity
Active sitei872 – 8721O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciARA:AT5G55300-MONOMER.
ARA:GQT-376-MONOMER.
BRENDAi5.99.1.2. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Gene namesi
Name:TOP1
Ordered Locus Names:At5g55300
ORF Names:MTE17.1
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G55300.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 916916DNA topoisomerase 1PRO_0000145206Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei170 – 1701Phosphoserine2 Publications
Modified residuei286 – 2861Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP30181.
PRIDEiP30181.

Interactioni

Protein-protein interaction databases

BioGridi20867. 2 interactions.
IntActiP30181. 2 interactions.
STRINGi3702.AT5G55300.2.

Structurei

3D structure databases

ProteinModelPortaliP30181.
SMRiP30181. Positions 367-913.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni577 – 5782Interaction with DNABy similarity
Regioni640 – 6456Interaction with DNABy similarity
Regioni731 – 7333Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type IB topoisomerase family.Curated

Phylogenomic databases

eggNOGiCOG3569.
HOGENOMiHOG000105469.
InParanoidiP30181.
KOiK03163.
PhylomeDBiP30181.

Family and domain databases

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.
PIRiS22864.
RefSeqiNP_200341.1. NM_124912.4. [P30181-1]
UniGeneiAt.197.

Genome annotation databases

EnsemblPlantsiAT5G55300.1; AT5G55300.1; AT5G55300. [P30181-1]
GeneIDi835623.
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.
PIRiS22864.
RefSeqiNP_200341.1. NM_124912.4. [P30181-1]
UniGeneiAt.197.

3D structure databases

ProteinModelPortaliP30181.
SMRiP30181. Positions 367-913.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi20867. 2 interactions.
IntActiP30181. 2 interactions.
STRINGi3702.AT5G55300.2.

Proteomic databases

PaxDbiP30181.
PRIDEiP30181.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT5G55300.

Phylogenomic databases

eggNOGiCOG3569.
HOGENOMiHOG000105469.
InParanoidiP30181.
KOiK03163.
PhylomeDBiP30181.

Enzyme and pathway databases

BioCyciARA:AT5G55300-MONOMER.
ARA:GQT-376-MONOMER.
BRENDAi5.99.1.2. 399.

Miscellaneous databases

PROiP30181.

Family and domain databases

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...

Publicationsi

« Hide 'large scale' publications
  1. Kieber J.K., Signer E.R.
    Submitted (SEP-1990) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones."
    Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N., Tabata S.
    DNA Res. 5:297-308(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-170, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Root.
  5. "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana."
    Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E., Rathjen J.P., Peck S.C.
    J. Proteomics 72:439-451(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-170, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: cv. Columbia.
  6. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
    Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
    Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-286, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiTOP1_ARATH
AccessioniPrimary (citable) accession number: P30181
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: June 24, 2015
This is version 115 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

External Data

Dasty 3

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 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.