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P04786

- TOP1_YEAST

UniProt

P04786 - TOP1_YEAST

Protein

DNA topoisomerase 1

Gene

TOP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 155 (01 Oct 2014)
      Sequence version 2 (01 Nov 1990)
      Previous versions | rss
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    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
    Sitei296 – 2961Interaction with DNABy similarity
    Sitei344 – 3441Interaction with DNABy similarity
    Sitei375 – 3751Interaction with DNABy similarity
    Sitei432 – 4321Interaction with DNABy similarity
    Sitei458 – 4581Interaction with DNABy similarity
    Sitei501 – 5011Interaction with DNABy similarity
    Sitei558 – 5581Interaction with DNABy similarity
    Active sitei727 – 7271O-(3'-phospho-DNA)-tyrosine intermediate2 PublicationsPROSITE-ProRule annotation

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: SGD
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro

    GO - Biological processi

    1. chromatin assembly or disassembly Source: SGD
    2. chromatin silencing at rDNA Source: SGD
    3. DNA strand elongation involved in DNA replication Source: SGD
    4. DNA topological change Source: SGD
    5. mitotic chromosome condensation Source: SGD
    6. nuclear migration Source: SGD
    7. regulation of mitotic recombination Source: SGD
    8. regulation of transcription from RNA polymerase II promoter Source: SGD
    9. transcription elongation from RNA polymerase II promoter Source: SGD

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33423-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1 (EC:5.99.1.2)
    Alternative name(s):
    DNA topoisomerase I
    Maintenance of killer protein 1
    Gene namesi
    Name:TOP1
    Synonyms:MAK1
    Ordered Locus Names:YOL006C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XV

    Organism-specific databases

    CYGDiYOL006c.
    SGDiS000005366. TOP1.

    Subcellular locationi

    Nucleusnucleolus. Nucleusnucleoplasm
    Note: Diffuse nuclear localization with some enrichment in nucleoli. On CPT treatment, cleared from nucleoli into nucleoplasm. Sumolyated forms found in both nucleoplasm and nucleoli By similarity.By similarity

    GO - Cellular componenti

    1. nucleolus Source: SGD
    2. nucleoplasm Source: UniProtKB-SubCell
    3. nucleus Source: SGD
    4. replication fork protection complex Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 769769DNA topoisomerase 1PRO_0000145211Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei14 – 141Phosphoserine3 Publications
    Modified residuei15 – 151Phosphoserine3 Publications
    Modified residuei24 – 241Phosphoserine1 Publication
    Modified residuei49 – 491Phosphoserine1 Publication
    Cross-linki65 – 65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
    Modified residuei76 – 761Phosphoserine3 Publications
    Cross-linki91 – 91Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)Curated

    Post-translational modificationi

    Sumoylated. Sumoylation plays a role in partitioning TOP1 between nucleoli and nucleoplasm By similarity.By similarity

    Keywords - PTMi

    Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP04786.
    PaxDbiP04786.
    PeptideAtlasiP04786.

    Expressioni

    Gene expression databases

    GenevestigatoriP04786.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    BioGridi34398. 443 interactions.
    DIPiDIP-1705N.
    IntActiP04786. 6 interactions.
    MINTiMINT-386768.
    STRINGi4932.YOL006C.

    Structurei

    Secondary structure

    1
    769
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi168 – 1703
    Beta strandi173 – 1753
    Helixi179 – 19012
    Turni191 – 1933
    Helixi196 – 1983
    Helixi200 – 21617
    Helixi229 – 2313
    Helixi235 – 24814
    Helixi256 – 27116
    Beta strandi272 – 2754
    Beta strandi278 – 2836
    Turni300 – 3034
    Helixi311 – 3133
    Beta strandi315 – 3173
    Beta strandi320 – 3223
    Beta strandi334 – 3374
    Beta strandi345 – 3495
    Turni351 – 3533
    Beta strandi356 – 3616

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1OISX-ray1.90A141-363[»]
    ProteinModelPortaliP04786.
    SMRiP04786. Positions 129-635, 676-769.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04786.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni357 – 3582Interaction with DNABy similarity
    Regioni420 – 4256Interaction with DNABy similarity
    Regioni512 – 5143Interaction with DNABy similarity

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi16 – 205Poly-Asp
    Compositional biasi55 – 13682Lys-richAdd
    BLAST
    Compositional biasi105 – 13935Glu-richAdd
    BLAST

    Sequence similaritiesi

    Belongs to the type IB topoisomerase family.Curated

    Phylogenomic databases

    eggNOGiCOG3569.
    GeneTreeiENSGT00390000016347.
    HOGENOMiHOG000105469.
    KOiK03163.
    OMAiHIDNIRT.
    OrthoDBiEOG7966R0.

    Family and domain databases

    Gene3Di1.10.10.41. 1 hit.
    1.10.132.10. 2 hits.
    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.

    P04786-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTIADASKVN HELSSDDDDD VPLSQTLKKR KVASMNSASL QDEAEPYDSD    50
    EAISKISKKK TKKIKTEPVQ SSSLPSPPAK KSATSKPKKI KKEDGDVKVK 100
    TTKKEEQENE KKKREEEEEE DKKAKEEEEE YKWWEKENED DTIKWVTLKH 150
    NGVIFPPPYQ PLPSHIKLYY DGKPVDLPPQ AEEVAGFFAA LLESDHAKNP 200
    VFQKNFFNDF LQVLKESGGP LNGIEIKEFS RCDFTKMFDY FQLQKEQKKQ 250
    LTSQEKKQIR LEREKFEEDY KFCELDGRRE QVGNFKVEPP DLFRGRGAHP 300
    KTGKLKRRVN PEDIVLNLSK DAPVPPAPEG HKWGEIRHDN TVQWLAMWRE 350
    NIFNSFKYVR LAANSSLKGQ SDYKKFEKAR QLKSYIDAIR RDYTRNLKSK 400
    VMLERQKAVA IYLIDVFALR AGGEKSEDEA DTVGCCSLRY EHVTLKPPNT 450
    VIFDFLGKDS IRFYQEVEVD KQVFKNLTIF KRPPKQPGHQ LFDRLDPSIL 500
    NKYLQNYMPG LTAKVFRTYN ASKTMQDQLD LIPNKGSVAE KILKYNAANR 550
    TVAILCNHQR TVTKGHAQTV EKANNRIQEL EWQKIRCKRA ILQLDKDLLK 600
    KEPKYFEEID DLTKEDEATI HKRIIDREIE KYQRKFVREN DKRKFEKEEL 650
    LPESQLKEWL EKVDEKKQEF EKELKTGEVE LKSSWNSVEK IKAQVEKLEQ 700
    RIQTSSIQLK DKEENSQVSL GTSKINYIDP RLSVVFCKKY DVPIEKIFTK 750
    TLREKFKWAI ESVDENWRF 769
    Length:769
    Mass (Da):89,995
    Last modified:November 1, 1990 - v2
    Checksum:i1FBD5FCED044C4A2
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K03077 Genomic DNA. Translation: AAA35162.1.
    Z74748 Genomic DNA. Translation: CAA99005.1.
    BK006948 Genomic DNA. Translation: DAA10777.1.
    PIRiA23161. ISBYT1.
    RefSeqiNP_014637.1. NM_001183260.1.

    Genome annotation databases

    EnsemblFungiiYOL006C; YOL006C; YOL006C.
    GeneIDi854156.
    KEGGisce:YOL006C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    K03077 Genomic DNA. Translation: AAA35162.1 .
    Z74748 Genomic DNA. Translation: CAA99005.1 .
    BK006948 Genomic DNA. Translation: DAA10777.1 .
    PIRi A23161. ISBYT1.
    RefSeqi NP_014637.1. NM_001183260.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1OIS X-ray 1.90 A 141-363 [» ]
    ProteinModelPortali P04786.
    SMRi P04786. Positions 129-635, 676-769.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34398. 443 interactions.
    DIPi DIP-1705N.
    IntActi P04786. 6 interactions.
    MINTi MINT-386768.
    STRINGi 4932.YOL006C.

    Chemistry

    ChEMBLi CHEMBL5948.

    Proteomic databases

    MaxQBi P04786.
    PaxDbi P04786.
    PeptideAtlasi P04786.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YOL006C ; YOL006C ; YOL006C .
    GeneIDi 854156.
    KEGGi sce:YOL006C.

    Organism-specific databases

    CYGDi YOL006c.
    SGDi S000005366. TOP1.

    Phylogenomic databases

    eggNOGi COG3569.
    GeneTreei ENSGT00390000016347.
    HOGENOMi HOG000105469.
    KOi K03163.
    OMAi HIDNIRT.
    OrthoDBi EOG7966R0.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33423-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P04786.
    NextBioi 975920.
    PROi P04786.

    Gene expression databases

    Genevestigatori P04786.

    Family and domain databases

    Gene3Di 1.10.10.41. 1 hit.
    1.10.132.10. 2 hits.
    2.170.11.10. 2 hits.
    3.90.15.10. 1 hit.
    InterProi IPR011010. 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 ]
    Pfami PF14370. Topo_C_assoc. 1 hit.
    PF01028. Topoisom_I. 1 hit.
    PF02919. Topoisom_I_N. 1 hit.
    [Graphical view ]
    PRINTSi PR00416. EUTPISMRASEI.
    SMARTi SM00435. TOPEUc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56349. SSF56349. 2 hits.
    SSF56741. SSF56741. 1 hit.
    PROSITEi PS00176. TOPOISOMERASE_I_EUK. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, characterization, and sequence of the yeast DNA topoisomerase I gene."
      Thrash C., Bankier A.T., Barrell B.G., Sternglanz R.
      Proc. Natl. Acad. Sci. U.S.A. 82:4374-4378(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Peptide sequencing and site-directed mutagenesis identify tyrosine-727 as the active site tyrosine of Saccharomyces cerevisiae DNA topoisomerase I."
      Lynn R.M., Bjornsti M.-A., Caron P.R., Wang J.C.
      Proc. Natl. Acad. Sci. U.S.A. 86:3559-3563(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE TYR-727.
    5. "Mapping of the active site tyrosine of eukaryotic DNA topoisomerase I."
      Eng W.-K., Pandit S.D., Sternglanz R.
      J. Biol. Chem. 264:13373-13376(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE TYR-727.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "A proteomic strategy for gaining insights into protein sumoylation in yeast."
      Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D., Gygi S.P.
      Mol. Cell. Proteomics 4:246-254(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUMOYLATION [LARGE SCALE ANALYSIS].
      Strain: EJY251-11b.
    8. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15 AND SER-76, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15; SER-24 AND SER-76, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15; SER-49 AND SER-76, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications."
      Lue N., Sharma A., Mondragon A., Wang J.C.
      Structure 3:1315-1322(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-363.

    Entry informationi

    Entry nameiTOP1_YEAST
    AccessioniPrimary (citable) accession number: P04786
    Secondary accession number(s): D6W261
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: November 1, 1990
    Last modified: October 1, 2014
    This is version 155 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In yeast, topoisomerase I seems to be dispensable. This is thought to be due to the abundant presence of topoisomerase II that can substitute for the relaxing activity of topoisomerase I.
    Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils.
    Present with 2970 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    External Data

    Dasty 3