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P04786 (TOP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 154. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA topoisomerase 1

EC=5.99.1.2
Alternative name(s):
DNA topoisomerase I
Maintenance of killer protein 1
Gene names
Name:TOP1
Synonyms:MAK1
Ordered Locus Names:YOL006C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length769 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Subunit structure

Monomer.

Subcellular location

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.

Post-translational modification

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

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.

Sequence similarities

Belongs to the type IB topoisomerase family.

Ontologies

Keywords
   Cellular componentNucleus
   LigandDNA-binding
   Molecular functionIsomerase
Topoisomerase
   PTMIsopeptide bond
Phosphoprotein
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA strand elongation involved in DNA replication

Inferred from mutant phenotype PubMed 2549254. Source: SGD

DNA topological change

Inferred from direct assay PubMed 6088500. Source: SGD

chromatin assembly or disassembly

Inferred from mutant phenotype PubMed 9199287. Source: SGD

chromatin silencing at rDNA

Inferred from mutant phenotype PubMed 10082585. Source: SGD

mitotic chromosome condensation

Inferred from mutant phenotype PubMed 8895658. Source: SGD

nuclear migration

Inferred from mutant phenotype PubMed 8895658. Source: SGD

regulation of mitotic recombination

Inferred from mutant phenotype PubMed 2902925. Source: SGD

regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 1660829. Source: SGD

transcription elongation from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 2840207. Source: SGD

   Cellular_componentnucleolus

Inferred from physical interaction PubMed 10967121. Source: SGD

nucleoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from direct assay PubMed 6088500. Source: SGD

replication fork protection complex

Inferred from direct assay PubMed 16531994. Source: SGD

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA topoisomerase type I activity

Inferred from direct assay PubMed 6088500. Source: SGD

DNA topoisomerase type II (ATP-hydrolyzing) activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 769769DNA topoisomerase 1
PRO_0000145211

Regions

Region357 – 3582Interaction with DNA By similarity
Region420 – 4256Interaction with DNA By similarity
Region512 – 5143Interaction with DNA By similarity
Compositional bias16 – 205Poly-Asp
Compositional bias55 – 13682Lys-rich
Compositional bias105 – 13935Glu-rich

Sites

Active site7271O-(3'-phospho-DNA)-tyrosine intermediate Ref.4 Ref.5
Site2961Interaction with DNA By similarity
Site3441Interaction with DNA By similarity
Site3751Interaction with DNA By similarity
Site4321Interaction with DNA By similarity
Site4581Interaction with DNA By similarity
Site5011Interaction with DNA By similarity
Site5581Interaction with DNA By similarity

Amino acid modifications

Modified residue141Phosphoserine Ref.8 Ref.9 Ref.10
Modified residue151Phosphoserine Ref.8 Ref.9 Ref.10
Modified residue241Phosphoserine Ref.9
Modified residue491Phosphoserine Ref.10
Modified residue761Phosphoserine Ref.8 Ref.9 Ref.10
Cross-link65Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) By similarity
Cross-link91Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Secondary structure

..................................... 769
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04786 [UniParc].

Last modified November 1, 1990. Version 2.
Checksum: 1FBD5FCED044C4A2

FASTA76989,995
        10         20         30         40         50         60 
MTIADASKVN HELSSDDDDD VPLSQTLKKR KVASMNSASL QDEAEPYDSD EAISKISKKK 

        70         80         90        100        110        120 
TKKIKTEPVQ SSSLPSPPAK KSATSKPKKI KKEDGDVKVK TTKKEEQENE KKKREEEEEE 

       130        140        150        160        170        180 
DKKAKEEEEE YKWWEKENED DTIKWVTLKH NGVIFPPPYQ PLPSHIKLYY DGKPVDLPPQ 

       190        200        210        220        230        240 
AEEVAGFFAA LLESDHAKNP VFQKNFFNDF LQVLKESGGP LNGIEIKEFS RCDFTKMFDY 

       250        260        270        280        290        300 
FQLQKEQKKQ LTSQEKKQIR LEREKFEEDY KFCELDGRRE QVGNFKVEPP DLFRGRGAHP 

       310        320        330        340        350        360 
KTGKLKRRVN PEDIVLNLSK DAPVPPAPEG HKWGEIRHDN TVQWLAMWRE NIFNSFKYVR 

       370        380        390        400        410        420 
LAANSSLKGQ SDYKKFEKAR QLKSYIDAIR RDYTRNLKSK VMLERQKAVA IYLIDVFALR 

       430        440        450        460        470        480 
AGGEKSEDEA DTVGCCSLRY EHVTLKPPNT VIFDFLGKDS IRFYQEVEVD KQVFKNLTIF 

       490        500        510        520        530        540 
KRPPKQPGHQ LFDRLDPSIL NKYLQNYMPG LTAKVFRTYN ASKTMQDQLD LIPNKGSVAE 

       550        560        570        580        590        600 
KILKYNAANR TVAILCNHQR TVTKGHAQTV EKANNRIQEL EWQKIRCKRA ILQLDKDLLK 

       610        620        630        640        650        660 
KEPKYFEEID DLTKEDEATI HKRIIDREIE KYQRKFVREN DKRKFEKEEL LPESQLKEWL 

       670        680        690        700        710        720 
EKVDEKKQEF EKELKTGEVE LKSSWNSVEK IKAQVEKLEQ RIQTSSIQLK DKEENSQVSL 

       730        740        750        760 
GTSKINYIDP RLSVVFCKKY DVPIEKIFTK TLREKFKWAI ESVDENWRF 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K03077 Genomic DNA. Translation: AAA35162.1.
Z74748 Genomic DNA. Translation: CAA99005.1.
BK006948 Genomic DNA. Translation: DAA10777.1.
PIRISBYT1. A23161.
RefSeqNP_014637.1. NM_001183260.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1OISX-ray1.90A141-363[»]
ProteinModelPortalP04786.
SMRP04786. Positions 129-635, 676-769.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34398. 443 interactions.
DIPDIP-1705N.
IntActP04786. 6 interactions.
MINTMINT-386768.
STRING4932.YOL006C.

Chemistry

ChEMBLCHEMBL5948.

Proteomic databases

MaxQBP04786.
PaxDbP04786.
PeptideAtlasP04786.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOL006C; YOL006C; YOL006C.
GeneID854156.
KEGGsce:YOL006C.

Organism-specific databases

CYGDYOL006c.
SGDS000005366. TOP1.

Phylogenomic databases

eggNOGCOG3569.
GeneTreeENSGT00390000016347.
HOGENOMHOG000105469.
KOK03163.
OMAHIDNIRT.
OrthoDBEOG7966R0.

Enzyme and pathway databases

BioCycYEAST:G3O-33423-MONOMER.

Gene expression databases

GenevestigatorP04786.

Family and domain databases

Gene3D1.10.10.41. 1 hit.
1.10.132.10. 2 hits.
2.170.11.10. 2 hits.
3.90.15.10. 1 hit.
InterProIPR011010. 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]
PfamPF14370. Topo_C_assoc. 1 hit.
PF01028. Topoisom_I. 1 hit.
PF02919. Topoisom_I_N. 1 hit.
[Graphical view]
PRINTSPR00416. EUTPISMRASEI.
SMARTSM00435. TOPEUc. 1 hit.
[Graphical view]
SUPFAMSSF56349. SSF56349. 2 hits.
SSF56741. SSF56741. 1 hit.
PROSITEPS00176. TOPOISOMERASE_I_EUK. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP04786.
NextBio975920.
PROP04786.

Entry information

Entry nameTOP1_YEAST
AccessionPrimary (citable) accession number: P04786
Secondary accession number(s): D6W261
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references