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P04786

- TOP1_YEAST

UniProt

P04786 - TOP1_YEAST

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Protein
DNA topoisomerase 1
Gene
TOP1, MAK1, YOL006C
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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 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.

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei296 – 2961Interaction with DNA By similarity
Sitei344 – 3441Interaction with DNA By similarity
Sitei375 – 3751Interaction with DNA By similarity
Sitei432 – 4321Interaction with DNA By similarity
Sitei458 – 4581Interaction with DNA By similarity
Sitei501 – 5011Interaction with DNA By similarity
Sitei558 – 5581Interaction with DNA By similarity
Active sitei727 – 7271O-(3'-phospho-DNA)-tyrosine intermediate2 Publications

GO - Molecular functioni

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

GO - Biological processi

  1. DNA strand elongation involved in DNA replication Source: SGD
  2. DNA topological change Source: SGD
  3. chromatin assembly or disassembly Source: SGD
  4. chromatin silencing at rDNA 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
Complete GO annotation...

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.

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 769769DNA topoisomerase 1
PRO_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) Inferred

Post-translational modificationi

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

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.

Miscellaneous databases

EvolutionaryTraceiP04786.

Family & Domainsi

Region

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

Compositional bias

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

Sequence similaritiesi

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 154 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.

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

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