Reviewed, UniProtKB/Swiss-Prot P04786 (TOP1_YEAST)

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	769 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	The reaction catalyzed by topoisomerases leads to the conversion of one topological isomer of DNA to another.
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit structure	Monomer.
Subcellular location	Nucleus › nucleolus. Nucleus › nucleoplasm. 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. When a topoisomerase transiently breaks a DNA backbone bond, it simultaneously forms a protein-DNA link, in which a tyrosyl oxygen in the enzyme is joined to a DNA phosphorus at one end of the enzyme-severed DNA strand. Present with 2970 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the eukaryotic type I topoisomerase family.

Ontologies

Keywords
Cellular component	Nucleus
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA strand elongation during DNA replication Inferred from mutant phenotype. Source: SGD DNA topological change Ref.1 Inferred from direct assay. Source: SGD DNA unwinding during replication Inferred from electronic annotation. Source: InterPro RNA elongation from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD chromatin assembly or disassembly Inferred from mutant phenotype. Source: SGD chromatin silencing at rDNA Inferred from mutant phenotype. Source: SGD mitotic chromosome condensation Inferred from genetic interaction. Source: SGD nuclear migration Inferred from genetic interaction. Source: SGD regulation of mitotic recombination Inferred from mutant phenotype. Source: SGD regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD
Cellular component	nucleolus Inferred from physical interaction. Source: SGD nucleoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell replication fork protection complex Inferred from direct assay. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro DNA topoisomerase type I activity Ref.1 Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
TRI1	Q05024	1	EBI-19338,EBI-27496

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 769

769

DNA topoisomerase 1

PRO_0000145211

Regions

Compositional bias

16 – 20

5

Poly-Asp

Compositional bias

55 – 136

82

Lys-rich

Compositional bias

105 – 139

35

Glu-rich

Sites

Active site

727

1

O-(3'-phospho-DNA)-tyrosine intermediate Ref.3 Ref.4

Amino acid modifications

Modified residue

14

1

Phosphoserine Ref.7 Ref.8 Ref.9

Modified residue

15

1

Phosphoserine Ref.7 Ref.8 Ref.9

Modified residue

24

1

Phosphoserine Ref.9

Modified residue

49

1

Phosphoserine Ref.8 Ref.9

Modified residue

54

1

Phosphoserine Ref.9

Modified residue

76

1

Phosphoserine Ref.7 Ref.9

Cross-link

65

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) By similarity

Cross-link

91

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Probable

Secondary structure

1

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769

Helix Strand Turn

Details...

Beta strand

168 – 170

3

Beta strand

173 – 175

3

Helix

179 – 190

12

Turn

191 – 193

3

Helix

196 – 198

3

Helix

200 – 216

17

Helix

229 – 231

3

Helix

235 – 248

14

Helix

256 – 271

16

Beta strand

272 – 275

4

Beta strand

278 – 283

6

Turn

300 – 303

4

Helix

311 – 313

3

Beta strand

315 – 317

3

Beta strand

320 – 322

3

Beta strand

334 – 337

4

Beta strand

345 – 349

5

Turn

351 – 353

3

Beta strand

356 – 361

6

Sequences

	Sequence		Length	Mass (Da)
	P04786-1 [UniParc]. Last modified November 1, 1990. Version 2. Checksum: 1FBD5FCED044C4A2	FASTA	769	89,995
	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

References

	« Hide 'large scale' referencesShow '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: 2989818] [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: 9169874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"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: 2542938] [Abstract] Cited for: ACTIVE SITE TYR-727.
[4]	"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: 2547758] [Abstract] Cited for: ACTIVE SITE TYR-727.
[5]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"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: 15542864] [Abstract] Cited for: SUMOYLATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[7]	"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: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15 AND SER-76, MASS SPECTROMETRY.
[8]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15 AND SER-49, MASS SPECTROMETRY.
[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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-14; SER-15; SER-24; SER-49; SER-54 AND SER-76, MASS SPECTROMETRY.
[10]	"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: 8747458] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-363.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

K03077 Genomic DNA. Translation: AAA35162.1.
Z74748 Genomic DNA. Translation: CAA99005.1.

PIR

ISBYT1. A23161.

RefSeq

NP_014637.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OIS	X-ray	1.90	A	141-363	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:1705N.

IntAct

P04786. 19 interactions.

STRING

P04786.

Proteomic databases

PeptideAtlas

P04786.

PRIDE

P04786.

Genome annotation databases

Ensembl

YOL006C; YOL006C; YOL006C; Saccharomyces cerevisiae. [Genome view]

GeneID

854156.

GenomeReviews

Gene locus YOL006C in contig Y13140_GR.

KEGG

sce:YOL006C.

NMPDR

fig|4932.3.peg.5732.

Organism-specific databases

CYGD

YOL006c.

SGD

S000005366. TOP1.

Phylogenomic databases

HOGENOM

P04786.

OMA

AVMKDTD.

Enzyme and pathway databases

BRENDA

5.99.1.2. 250.

Gene expression databases

ArrayExpress

P04786.

Genevestigator

P04786.

GermOnline

YOL006C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR018521. TopoI_AS.
IPR001631. TopoI_C.
IPR013499. TopoI_C_euk.
IPR014711. TopoI_cat_a-hlx-sub_euk.
IPR014727. TopoI_cat_a/b-sub_euk.
IPR013500. TopoI_cat_euk.
IPR013030. TopoI_DNA-bd_mixed-a/b_euk.
IPR008336. TopoI_DNA_bd_euk.
[Graphical view]

Gene3D

G3DSA:3.90.15.10. TopoI_cat_a-hlx-sub_euk. 1 hit.
G3DSA:1.10.132.10. TopoI_cat_a/b-sub_euk. 1 hit.
G3DSA:2.170.11.10. TopoI_DNA-bd_mixed-a/b_euk. 1 hit.

Pfam

PF01028. Topoisom_I. 1 hit.
PF02919. Topoisom_I_N. 1 hit.
[Graphical view]

PRINTS

PR00416. EUTPISMRASEI.

SMART

SM00435. TOPEUc. 1 hit.
[Graphical view]

PROSITE

PS00176. TOPOISOMERASE_I_EUK. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

975920.

Entry information

Entry name

TOP1_YEAST

Accession

Primary (citable) accession number: P04786

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	November 1, 1990
Last modified:	November 3, 2009
This is version 103 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)