TOP1_YEAST
ID TOP1_YEAST Reviewed; 769 AA.
AC P04786; D6W261;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1990, sequence version 2.
DT 03-AUG-2022, entry version 215.
DE RecName: Full=DNA topoisomerase 1;
DE EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10130};
DE AltName: Full=DNA topoisomerase I;
DE AltName: Full=Maintenance of killer protein 1;
GN Name=TOP1; Synonyms=MAK1; OrderedLocusNames=YOL006C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2989818; DOI=10.1073/pnas.82.13.4374;
RA Thrash C., Bankier A.T., Barrell B.G., Sternglanz R.;
RT "Cloning, characterization, and sequence of the yeast DNA topoisomerase I
RT gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 82:4374-4378(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP ACTIVE SITE TYR-727.
RX PubMed=2542938; DOI=10.1073/pnas.86.10.3559;
RA Lynn R.M., Bjornsti M.-A., Caron P.R., Wang J.C.;
RT "Peptide sequencing and site-directed mutagenesis identify tyrosine-727 as
RT the active site tyrosine of Saccharomyces cerevisiae DNA topoisomerase I.";
RL Proc. Natl. Acad. Sci. U.S.A. 86:3559-3563(1989).
RN [5]
RP ACTIVE SITE TYR-727.
RX PubMed=2547758; DOI=10.1016/s0021-9258(18)80002-3;
RA Eng W.-K., Pandit S.D., Sternglanz R.;
RT "Mapping of the active site tyrosine of eukaryotic DNA topoisomerase I.";
RL J. Biol. Chem. 264:13373-13376(1989).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15 AND SER-76, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15; SER-24 AND
RP SER-76, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15; SER-49 AND
RP SER-76, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-363.
RX PubMed=8747458; DOI=10.1016/s0969-2126(01)00269-6;
RA Lue N., Sharma A., Mondragon A., Wang J.C.;
RT "A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure
RT and mechanistic implications.";
RL Structure 3:1315-1322(1995).
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA
CC introduced during the DNA replication and transcription by transiently
CC cleaving and rejoining one strand of the DNA duplex. Introduces a
CC single-strand break via transesterification at a target site in duplex
CC DNA. The scissile phosphodiester is attacked by the catalytic tyrosine
CC of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-
CC enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free
CC DNA strand then rotates around the intact phosphodiester bond on the
CC opposing strand, thus removing DNA supercoils. Finally, in the
CC religation step, the DNA 5'-OH attacks the covalent intermediate to
CC expel the active-site tyrosine and restore the DNA phosphodiester
CC backbone (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10130};
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus. Nucleus, nucleoplasm.
CC Note=Diffuse nuclear localization with some enrichment in nucleoli. On
CC CPT treatment, cleared from nucleoli into nucleoplasm. Sumoylated forms
CC found in both nucleoplasm and nucleoli (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: In yeast, topoisomerase I seems to be dispensable. This
CC is thought to be due to the abundant presence of topoisomerase II that
CC can substitute for the relaxing activity of topoisomerase I.
CC -!- MISCELLANEOUS: Eukaryotic topoisomerase I and II can relax both
CC negative and positive supercoils, whereas prokaryotic enzymes relax
CC only negative supercoils.
CC -!- MISCELLANEOUS: Present with 2970 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the type IB topoisomerase family. {ECO:0000305}.
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DR EMBL; K03077; AAA35162.1; -; Genomic_DNA.
DR EMBL; Z74748; CAA99005.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10777.1; -; Genomic_DNA.
DR PIR; A23161; ISBYT1.
DR RefSeq; NP_014637.1; NM_001183260.1.
DR PDB; 1OIS; X-ray; 1.90 A; A=141-363.
DR PDBsum; 1OIS; -.
DR AlphaFoldDB; P04786; -.
DR SMR; P04786; -.
DR BioGRID; 34398; 640.
DR DIP; DIP-1705N; -.
DR IntAct; P04786; 13.
DR MINT; P04786; -.
DR STRING; 4932.YOL006C; -.
DR BindingDB; P04786; -.
DR ChEMBL; CHEMBL5948; -.
DR iPTMnet; P04786; -.
DR MaxQB; P04786; -.
DR PaxDb; P04786; -.
DR PRIDE; P04786; -.
DR EnsemblFungi; YOL006C_mRNA; YOL006C; YOL006C.
DR GeneID; 854156; -.
DR KEGG; sce:YOL006C; -.
DR SGD; S000005366; TOP1.
DR VEuPathDB; FungiDB:YOL006C; -.
DR eggNOG; KOG0981; Eukaryota.
DR GeneTree; ENSGT00940000167650; -.
DR HOGENOM; CLU_009193_1_0_1; -.
DR InParanoid; P04786; -.
DR OMA; GLRYQKW; -.
DR BioCyc; YEAST:G3O-33423-MON; -.
DR Reactome; R-SCE-4615885; SUMOylation of DNA replication proteins.
DR EvolutionaryTrace; P04786; -.
DR PRO; PR:P04786; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; P04786; protein.
DR GO; GO:0005730; C:nucleolus; IPI:SGD.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0031298; C:replication fork protection complex; IDA:SGD.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IDA:SGD.
DR GO; GO:0006325; P:chromatin organization; IMP:SGD.
DR GO; GO:0007059; P:chromosome segregation; IBA:GO_Central.
DR GO; GO:0006260; P:DNA replication; IBA:GO_Central.
DR GO; GO:0006271; P:DNA strand elongation involved in DNA replication; IMP:SGD.
DR GO; GO:0006265; P:DNA topological change; IDA:SGD.
DR GO; GO:0007076; P:mitotic chromosome condensation; IMP:SGD.
DR GO; GO:0007097; P:nuclear migration; IMP:SGD.
DR GO; GO:0000183; P:rDNA heterochromatin assembly; IMP:SGD.
DR GO; GO:0000019; P:regulation of mitotic recombination; IMP:SGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0009303; P:rRNA transcription; IGI:SGD.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IMP:SGD.
DR CDD; cd00659; Topo_IB_C; 1.
DR Gene3D; 1.10.10.41; -; 1.
DR Gene3D; 1.10.132.10; -; 1.
DR Gene3D; 2.170.11.10; -; 1.
DR Gene3D; 3.90.15.10; -; 1.
DR InterPro; IPR011010; DNA_brk_join_enz.
DR InterPro; IPR013034; DNA_topo_DNA_db_N_dom1.
DR InterPro; IPR013030; DNA_topo_DNA_db_N_dom2.
DR InterPro; IPR001631; TopoI.
DR InterPro; IPR018521; TopoI_AS.
DR InterPro; IPR025834; TopoI_C_dom.
DR InterPro; IPR014711; TopoI_cat_a-hlx-sub_euk.
DR InterPro; IPR014727; TopoI_cat_a/b-sub_euk.
DR InterPro; IPR013500; TopoI_cat_euk.
DR InterPro; IPR008336; TopoI_DNA-bd_euk.
DR InterPro; IPR036202; TopoI_DNA-bd_euk_N_sf.
DR InterPro; IPR013499; TopoI_euk.
DR Pfam; PF14370; Topo_C_assoc; 1.
DR Pfam; PF01028; Topoisom_I; 1.
DR Pfam; PF02919; Topoisom_I_N; 1.
DR PRINTS; PR00416; EUTPISMRASEI.
DR SMART; SM00435; TOPEUc; 1.
DR SUPFAM; SSF56349; SSF56349; 1.
DR SUPFAM; SSF56741; SSF56741; 1.
DR PROSITE; PS00176; TOPOISOMERASE_I_EUK; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Isomerase; Nucleus; Phosphoprotein;
KW Reference proteome; Topoisomerase.
FT CHAIN 1..769
FT /note="DNA topoisomerase 1"
FT /id="PRO_0000145211"
FT REGION 1..132
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 357..358
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 420..425
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT REGION 512..514
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT COMPBIAS 10..26
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 29..43
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 87..132
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 727
FT /note="O-(3'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10130,
FT ECO:0000269|PubMed:2542938, ECO:0000269|PubMed:2547758"
FT SITE 296
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 344
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 375
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 432
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 501
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 558
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT MOD_RES 14
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 15
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 24
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 49
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 76
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT STRAND 168..170
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 179..190
FT /evidence="ECO:0007829|PDB:1OIS"
FT TURN 191..193
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 200..216
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 235..248
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 256..271
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 272..275
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 278..283
FT /evidence="ECO:0007829|PDB:1OIS"
FT TURN 300..303
FT /evidence="ECO:0007829|PDB:1OIS"
FT HELIX 311..313
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 320..322
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 334..337
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 345..349
FT /evidence="ECO:0007829|PDB:1OIS"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:1OIS"
FT STRAND 356..361
FT /evidence="ECO:0007829|PDB:1OIS"
SQ SEQUENCE 769 AA; 89995 MW; 1FBD5FCED044C4A2 CRC64;
MTIADASKVN HELSSDDDDD VPLSQTLKKR KVASMNSASL QDEAEPYDSD EAISKISKKK
TKKIKTEPVQ SSSLPSPPAK KSATSKPKKI KKEDGDVKVK TTKKEEQENE KKKREEEEEE
DKKAKEEEEE YKWWEKENED DTIKWVTLKH NGVIFPPPYQ PLPSHIKLYY DGKPVDLPPQ
AEEVAGFFAA LLESDHAKNP VFQKNFFNDF LQVLKESGGP LNGIEIKEFS RCDFTKMFDY
FQLQKEQKKQ LTSQEKKQIR LEREKFEEDY KFCELDGRRE QVGNFKVEPP DLFRGRGAHP
KTGKLKRRVN PEDIVLNLSK DAPVPPAPEG HKWGEIRHDN TVQWLAMWRE NIFNSFKYVR
LAANSSLKGQ SDYKKFEKAR QLKSYIDAIR RDYTRNLKSK VMLERQKAVA IYLIDVFALR
AGGEKSEDEA DTVGCCSLRY EHVTLKPPNT VIFDFLGKDS IRFYQEVEVD KQVFKNLTIF
KRPPKQPGHQ LFDRLDPSIL NKYLQNYMPG LTAKVFRTYN ASKTMQDQLD LIPNKGSVAE
KILKYNAANR TVAILCNHQR TVTKGHAQTV EKANNRIQEL EWQKIRCKRA ILQLDKDLLK
KEPKYFEEID DLTKEDEATI HKRIIDREIE KYQRKFVREN DKRKFEKEEL LPESQLKEWL
EKVDEKKQEF EKELKTGEVE LKSSWNSVEK IKAQVEKLEQ RIQTSSIQLK DKEENSQVSL
GTSKINYIDP RLSVVFCKKY DVPIEKIFTK TLREKFKWAI ESVDENWRF
