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Protein

DNA topoisomerase 1

Gene

top1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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. May play a role in the circadian transcription of the core circadian clock component ARNTL/BMAL1.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
Sitei372 – 3721Interaction with DNABy similarity
Sitei420 – 4201Interaction with DNABy similarity
Sitei468 – 4681Interaction with DNABy similarity
Sitei499 – 4991Interaction with DNABy similarity
Sitei557 – 5571Interaction with DNABy similarity
Sitei588 – 5881Interaction with DNABy similarity
Sitei630 – 6301Interaction with DNABy similarity
Sitei688 – 6881Interaction with DNABy similarity
Sitei706 – 7061Interaction with DNABy similarity
Active sitei779 – 7791O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation

GO - Molecular functioni

  1. core promoter sequence-specific DNA binding Source: UniProtKB
  2. DNA topoisomerase type I activity Source: UniProtKB-EC
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro

GO - Biological processi

  1. chromatin remodeling Source: UniProtKB
  2. circadian regulation of gene expression Source: UniProtKB
  3. DNA topological change Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Biological rhythms

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Gene namesi
Name:top1
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-950006. top1.1.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 829829DNA topoisomerase 1PRO_0000145204Add
BLAST

Proteomic databases

PRIDEiP41512.

Interactioni

Subunit structurei

Monomer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP41512.
SMRiP41512. Positions 255-808.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni481 – 4822Interaction with DNABy similarity
Regioni544 – 5496Interaction with DNABy similarity
Regioni641 – 6433Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type IB topoisomerase family.Curated

Phylogenomic databases

HOVERGENiHBG007988.
KOiK03163.

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.

P41512-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEDHVQNDS QIEAVFRVND SHKHKKDKEH RHKEHKKDKD REKSKHNNSE
60 70 80 90 100
HRDPSEKKHK DKHKNNDKHR EKDGEKHRER DGEKHRDKNG EKHRDGEKHK
110 120 130 140 150
EKDIEKHKEV EKHRVKDGEK HKEKDVEKHK EKDVEKHRDG EKHKHRDKDR
160 170 180 190 200
EKKKEEKMKS SSGGVKVKKE NGFSSPVRVK DEPEDQGFYV SPKENKAMKR
210 220 230 240 250
PREDDEDYKP KKIKSEDDKK GKKRKQEEED IKPKKKSKAK GNEEGVKKKK
260 270 280 290 300
VKKEEEEKWK WWEEERHRDG IKWKFLEHKG PVFAPPYEPV PDNVKFYYDG
310 320 330 340 350
NLVKLSPKAE EVATFFAKML DHEYTTKDIF RKNFFKDWKK EMTTDERNLI
360 370 380 390 400
TNLSKCDFNA MSLYFKEQSE ARKNMTKEEK LKIKAENERL LQEYGYCIMD
410 420 430 440 450
NHKERIANFR IEPPGLFRGR GDHPKMGKLK KRIMPEDIII NCSKDSKIPV
460 470 480 490 500
APAGHKWKEV RHDGKVTWLV SWTENIQGSI KYIMLNPSSR IKGEKDWQKY
510 520 530 540 550
ETARRLKMCV EKIRNTYKED WKSKEMKVRQ RAVALYFIDK LALRAGNEKE
560 570 580 590 600
EGETADTVGC CSLRVEHINL FQELDGQEFV VEFDFPGKDS IRYYNKVPVE
610 620 630 640 650
KRVFKNLQLF MENKQPDDDL FDRLNTSILN KHLQDLMEGL TAKVFRTYNA
660 670 680 690 700
SITLQQQLDE LTNSDDNVPA KILSYNRANR AVAILCNHQR APPKTFEKSM
710 720 730 740 750
MNLQGKIDAK KDQLADARRE FKSAKADAKV RRDEKTKKLV ESKKKAVQRI
760 770 780 790 800
EEQLMKLEVQ ATDREENKQI ALGTSKLNYL DPRISVAWCK KYGVPIEKIY
810 820
NKTQRKNLLG PSIWQTTTSN FNAEQRCFS
Length:829
Mass (Da):98,231
Last modified:October 31, 1995 - v1
Checksum:i8D1FE4252A916219
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07777 mRNA. Translation: AAB36608.1.
PIRiS72366.
RefSeqiNP_001084031.1. NM_001090562.1.
UniGeneiXl.62.

Genome annotation databases

GeneIDi399263.
KEGGixla:399263.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07777 mRNA. Translation: AAB36608.1.
PIRiS72366.
RefSeqiNP_001084031.1. NM_001090562.1.
UniGeneiXl.62.

3D structure databases

ProteinModelPortaliP41512.
SMRiP41512. Positions 255-808.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP41512.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi399263.
KEGGixla:399263.

Organism-specific databases

CTDi399263.
XenbaseiXB-GENE-950006. top1.1.

Phylogenomic databases

HOVERGENiHBG007988.
KOiK03163.

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

  1. "Cloning and characterization of the gene for the somatic form of DNA topoisomerase I from Xenopus laevis."
    Pandit S.D., Richard R.E., Sternglanz R., Bogenhagen D.F.
    Nucleic Acids Res. 24:3593-3600(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].

Entry informationi

Entry nameiTOP1_XENLA
AccessioniPrimary (citable) accession number: P41512
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 1995
Last sequence update: October 31, 1995
Last modified: January 6, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Documents

  1. 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.