P13099 (TOP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 3
EC=5.99.1.2

Alternative name(s):
DNA topoisomerase III

Gene names

Name:	TOP3
Synonyms:	EDR1
Ordered Locus Names:	YLR234W
ORF Names:	L8083.3

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	656 AA.
Sequence status	Complete.
Protein existence	Evidence 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-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone By similarity. Essential for proper chromosome segregation in both meiosis and mitosis. Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA. The TOP3-SGS1 protein complex may function as a eukaryotic reverse gyrase introducing positive supercoils into extrachromosomal ribosomal DNA rings. Ref.1
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit structure	Forms a complex with SGS1 and RMI1. Interacts with SGS1. Ref.6 Ref.7
Miscellaneous	Present with 468 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the type IA topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: InterPro mitotic sister chromatid cohesion Inferred from mutant phenotype. Source: SGD reciprocal meiotic recombination Inferred from genetic interaction. Source: SGD regulation of DNA recombination Inferred from mutant phenotype. Source: SGD telomere maintenance via telomerase Inferred from mutant phenotype. Source: SGD
Cellular component	RecQ helicase-Topo III complex Inferred from direct assay Ref.7. Source: SGD nucleus Inferred by curator. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase type I activity Inferred from direct assay. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 656	656	DNA topoisomerase 3		PRO_0000145198
Regions
	Domain	2 – 155	154	Toprim
Sites
	Active site	356	1	O-(5'-phospho-DNA)-tyrosine intermediate By similarity

Sequences

	Sequence		Length	Mass (Da)
	P13099 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: 51DF78936A88B4F4	FASTA	656	74,371
	10 20 30 40 50 60 MKVLCVAEKN SIAKAVSQIL GGGRSTSRDS GYMYVKNYDF MFSGFPFARN GANCEVTMTS 70 80 90 100 110 120 VAGHLTGIDF SHDSHGWGKC AIQELFDAPL NEIMNNNQKK IASNIKREAR NADYLMIWTD 130 140 150 160 170 180 CDREGEYIGW EIWQEAKRGN RLIQNDQVYR AVFSHLERQH ILNAARNPSR LDMKSVHAVG 190 200 210 220 230 240 TRIEIDLRAG VTFTRLLTET LRNKLRNQAT MTKDGAKHRG GNKNDSQVVS YGTCQFPTLG 250 260 270 280 290 300 FVVDRFERIR NFVPEEFWYI QLVVENKDNG GTTTFQWDRG HLFDRLSVLT FYETCIETAG 310 320 330 340 350 360 NVAQVVDLKS KPTTKYRPLP LTTVELQKNC ARYLRLNAKQ SLDAAEKLYQ KGFISYPRTE 370 380 390 400 410 420 TDTFPHAMDL KSLVEKQAQL DQLAAGGRTA WASYAASLLQ PENTSNNNKF KFPRSGSHDD 430 440 450 460 470 480 KAHPPIHPIV SLGPEANVSP VERRVYEYVA RHFLACCSED AKGQSMTLVL DWAVERFSAS 490 500 510 520 530 540 GLVVLERNFL DVYPWARWET TKQLPRLEMN ALVDIAKAEM KAGTTAPPKP MTESELILLM 550 560 570 580 590 600 DTNGIGTDAT IAEHIDKIQV RNYVRSEKVG KETYLQPTTL GVSLVHGFEA IGLEDSFAKP 610 620 630 640 650 FQRREMEQDL KKICEGHASK TDVVKDIVEK YRKYWHKTNA CKNTLLQVYD RVKASM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A hyper-recombination mutation in S. cerevisiae identifies a novel eukaryotic topoisomerase." Wallis J.W., Chrebet G., Brodsky G., Rolfe M., Rothstein R. Cell 58:409-419(1989) [PubMed: 2546682] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"An essential yeast protein, CBF5p, binds in vitro to centromeres and microtubules." Jiang W., Middleton K., Yoon H.-J., Fouquet C., Carbon J. Mol. Cell. Biol. 13:4884-4893(1993) [PubMed: 8336724] [Abstract] Cited for: PROTEIN SEQUENCE OF 578-592; 605-615; 794-805 AND 1038-1046.
[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]	"RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex." Chang M., Bellaoui M., Zhang C., Desai R., Morozov P., Delgado-Cruzata L., Rothstein R., Freyer G.A., Boone C., Brown G.W. EMBO J. 24:2024-2033(2005) [PubMed: 15889139] [Abstract] Cited for: SUBUNIT.
[7]	"Yeast Rmi1/Nce4 controls genome stability as a subunit of the Sgs1-Top3 complex." Mullen J.R., Nallaseth F.S., Lan Y.Q., Slagle C.E., Brill S.J. Mol. Cell. Biol. 25:4476-4487(2005) [PubMed: 15899853] [Abstract] Cited for: SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M24939 Genomic DNA. Translation: AAA35161.1. U19027 Genomic DNA. Translation: AAB67406.1. BK006945 Genomic DNA. Translation: DAA09550.1.
PIR	ISBYT3. A33169.
RefSeq	NP_013335.1. NM_001182121.1.
3D structure databases
ProteinModelPortal	P13099.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2912N.
IntAct	P13099. 3 interactions.
MINT	MINT-442624.
STRING	P13099.
Proteomic databases
PeptideAtlas	P13099.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YLR234W; YLR234W; YLR234W.
GeneID	850935.
KEGG	sce:YLR234W.
NMPDR	fig|4932.3.peg.4348.
Organism-specific databases
CYGD	YLR234w.
SGD	S000004224. TOP3.
Phylogenomic databases
eggNOG	fuNOG04177.
GeneTree	EFGT00050000000587.
HOGENOM	HBG525547.
OMA	AVDCRSE.
OrthoDB	EOG4KWP2D.
Gene expression databases
ArrayExpress	P13099.
Genevestigator	P13099.
GermOnline	YLR234W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR000380. Topo_IA. IPR003601. Topo_IA_2. IPR023406. Topo_IA_AS. IPR013497. Topo_IA_cen. IPR013824. Topo_IA_cen_sub1. IPR013826. Topo_IA_cen_sub3. IPR023405. Topo_IA_core_domain. IPR003602. Topo_IA_DNA-bd. IPR006171. Toprim_domain. [Graphical view]
Gene3D	G3DSA:1.10.460.10. Topo_IA_cen_sub1. 2 hits. G3DSA:1.10.290.10. Topo_IA_cen_sub3. 1 hit.
KO	K03165.
PANTHER	PTHR11390. Topo_IA. 1 hit.
Pfam	PF01131. Topoisom_bac. 1 hit. PF01751. Toprim. 1 hit. [Graphical view]
PRINTS	PR00417. PRTPISMRASEI.
SMART	SM00437. TOP1Ac. 1 hit. SM00436. TOP1Bc. 1 hit. SM00493. TOPRIM. 1 hit. [Graphical view]
SUPFAM	SSF56712. Topo_IA_core. 1 hit.
PROSITE	PS00396. TOPOISOMERASE_I_PROK. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	967378.

Entry information

Entry name

TOP3_YEAST

Accession

Primary (citable) accession number: P13099
Secondary accession number(s): D6VYN4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	December 14, 2011
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program