Q04437 (KU80_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent DNA helicase II subunit 2
EC=3.6.4.12

Alternative name(s):
ATP-dependent DNA helicase II subunit Ku80
High affinity DNA-binding factor subunit 2
Yeast Ku80

Gene names

Name:	YKU80
Synonyms:	HDF2
Ordered Locus Names:	YMR106C
ORF Names:	YM9718.05C

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	629 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Single stranded DNA-dependent ATP-dependent helicase. Involved in non-homologous end joining (NHEJ) DNA double strand break repair. DNA-binding is sequence-independent but has a high affinity to nicks in double stranded DNA and to the ends of duplex DNA. Binds to naturally occurring chromosomal ends, and therefore provides chromosomal end protection. Appears to have a role in recruitment of telomerase and CDC13 to the telomere and the subsequent telomere elongation. Required also for telomere recombination to repair telomeric ends in the absence of telomerase. KU70, of the KU70/KU80 heterodimer, binds to the stem loop of TLC1, the RNA component of telomerase. Involved in telomere maintenance. Interacts with telomeric repeats and subtelomeric sequences thereby controlling telomere length and protecting against subtelomeric rearrangement. Maintains telomeric chromatin, which is involved in silencing the expression of genes located at the telomere. Required for mating-type switching. Ref.4 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.18 Ref.19
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	Heterodimer of YKU70/HDF1 and YKU80/HDF2. Interacts with SIR4. Ref.4 Ref.5 Ref.18
Subcellular location	Nucleus. Chromosome › telomere Ref.8.
Miscellaneous	Present with 358 molecules/cell in log phase SD medium. Ref.17
Sequence similarities	Belongs to the ku80 family. Contains 1 Ku domain.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair
Cellular component	Chromosome Nucleus Telomere
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	chromatin assembly or disassembly Inferred from direct assay. Source: SGD chromatin silencing Inferred from mutant phenotype. Source: SGD donor selection Inferred from direct assay Ref.19. Source: SGD double-strand break repair via homologous recombination Inferred from mutant phenotype. Source: SGD double-strand break repair via nonhomologous end joining Inferred from direct assay. Source: SGD protein localization to chromosome Inferred from genetic interaction. Source: SGD telomere maintenance Inferred from mutant phenotype. Source: SGD
Cellular component	DNA-dependent protein kinase-DNA ligase 4 complex Inferred from electronic annotation. Source: InterPro Ku70:Ku80 complex Inferred from direct assay. Source: SGD nuclear telomeric heterochromatin Traceable author statement. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent DNA helicase activity Inferred from electronic annotation. Source: InterPro RNA binding Inferred from direct assay Ref.15. Source: SGD damaged DNA binding Traceable author statement. Source: SGD protein binding Inferred from physical interaction Ref.18. Source: IntAct telomeric DNA binding Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SIR4	P11978	2	EBI-8224,EBI-17237
YKU70	P32807	3	EBI-8224,EBI-8214

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 629	629	ATP-dependent DNA helicase II subunit 2		PRO_0000084339
Regions
	Domain	254 – 476	223	Ku
Natural variations
	Natural variant	149	1	L → V in strain: DBVPG6044, SK1 and YPS128.
	Natural variant	301	1	S → L in strain: DBVPG1853.
	Natural variant	349	1	N → D in strain: DBVPG6044, SK1 and YPS128.
	Natural variant	499	1	G → D in strain: DBVPG1853.
	Natural variant	518	1	E → A in strain: DBVPG6044, SK1 and YPS128.
	Natural variant	528	1	T → A in strain: DBVPG1853.
	Natural variant	585	1	I → S in strain: DBVPG6763.

Sequences

	Sequence		Length	Mass (Da)
	Q04437 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 58126164EE375643	FASTA	629	71,241
	10 20 30 40 50 60 MSSESTTFIV DVSPSMMKNN NVSKSMAYLE YTLLNKSKKS RKTDWISCYL ANCPVSENSQ 70 80 90 100 110 120 EIPNVFQIQS FLAPVTTTAT IGFIKRLKQY CDQHSHDSSN EGLQSMIQCL LVVSLDIKQQ 130 140 150 160 170 180 FQARKILKQI VVFTDNLDDL DITDEEIDLL TEELSTRIIL IDCGKDTQEE RKKSNWLKLV 190 200 210 220 230 240 EAIPNSRIYN MNELLVEITS PATSVVKPVR VFSGELRLGA DILSTQTSNP SGSMQDENCL 250 260 270 280 290 300 CIKVEAFPAT KAVSGLNRKT AVEVEDSQKK ERYVGVKSII EYEIHNEGNK KNVSEDDQSG 310 320 330 340 350 360 SSYIPVTISK DSVTKAYRYG ADYVVLPSVL VDQTVYESFP GLDLRGFLNR EALPRYFLTS 370 380 390 400 410 420 ESSFITADTR LGCQSDLMAF SALVDVMLEN RKIAVARYVS KKDSEVNMCA LCPVLIEHSN 430 440 450 460 470 480 INSEKKFVKS LTLCRLPFAE DERVTDFPKL LDRTTTSGVP LKKETDGHQI DELMEQFVDS 490 500 510 520 530 540 MDTDELPEIP LGNYYQPIGE VTTDTTLPLP SLNKDQEENK KDPLRIPTVF VYRQQQVLLE 550 560 570 580 590 600 WIHQLMINDS REFEIPELPD SLKNKISPYT HKKFDSTKLV EVLGIKKVDK LKLDSELKTE 610 620 LEREKIPDLE TLLKRGEQHS RGSPNNSNN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence diversity, reproductive isolation and species concepts in Saccharomyces." Liti G., Barton D.B., Louis E.J. Genetics 174:839-850(2006) [PubMed: 16951060] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: DBVPG1135, DBVPG1373, DBVPG1378, DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6044, DBVPG6763, DBVPG6765, SK1, Y55 and YPS128.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII." Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T., Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K., Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P. , Skelton J., Walsh S.V., Whitehead S., Barrell B.G. Nature 387:90-93(1997) [PubMed: 9169872] [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]	"HDF2, the second subunit of the Ku homologue from Saccharomyces cerevisiae." Feldmann H., Driller L., Meier B., Mages G., Kellermann J., Winnacker E.-L. J. Biol. Chem. 271:27765-27769(1996) [PubMed: 8910371] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, FUNCTION IN TELOMERE MAINTENANCE, SUBUNIT.
[5]	"A putative homologue of the human autoantigen Ku from Saccharomyces cerevisiae." Feldmann H., Winnacker E.L. J. Biol. Chem. 268:12895-12900(1993) [PubMed: 8509423] [Abstract] Cited for: SUBUNIT.
[6]	"Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance." Boulton S.J., Jackson S.P. Nucleic Acids Res. 24:4639-4648(1996) [PubMed: 8972848] [Abstract] Cited for: FUNCTION IN TELOMERE MAINTENANCE.
[7]	"Telomerase, Ku, and telomeric silencing in Saccharomyces cerevisiae." Evans S.K., Sistrunk M.L., Nugent C.I., Lundblad V. Chromosoma 107:352-358(1998) [PubMed: 9914366] [Abstract] Cited for: FUNCTION IN TELOMERIC GENE SILENCING.
[8]	"Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres." Laroche T., Martin S.G., Gotta M., Gorham H.C., Pryde F.E., Louis E.J., Gasser S.M. Curr. Biol. 8:653-656(1998) [PubMed: 9635192] [Abstract] Cited for: FUNCTION IN TELOMERE MAINTENANCE, SUBCELLULAR LOCATION.
[9]	"Telomere maintenance is dependent on activities required for end repair of double-strand breaks." Nugent C.I., Bosco G., Ross L.O., Evans S.K., Salinger A.P., Moore J.K., Haber J.E., Lundblad V. Curr. Biol. 8:657-660(1998) [PubMed: 9635193] [Abstract] Cited for: FUNCTION IN DOUBLE-STRAND DNA REPAIR AND TELOMERE MAINTENANCE.
[10]	"The yeast Ku heterodimer is essential for protection of the telomere against nucleolytic and recombinational activities." Polotnianka R.M., Li J., Lustig A.J. Curr. Biol. 8:831-834(1998) [PubMed: 9663392] [Abstract] Cited for: FUNCTION IN TELOMERE MAINTENANCE.
[11]	"Yeast Ku as a regulator of chromosomal DNA end structure." Gravel S., Larrivee M., Labrecque P., Wellinger R.J. Science 280:741-744(1998) [PubMed: 9563951] [Abstract] Cited for: FUNCTION IN CHROMOSOME END PROTECTION AND TELOMERE MAINTENANCE.
[12]	"The Saccharomyces cerevisiae DNA damage checkpoint is required for efficient repair of double strand breaks by non-homologous end joining." de la Torre-Ruiz M., Lowndes N.F. FEBS Lett. 467:311-315(2000) [PubMed: 10675560] [Abstract] Cited for: FUNCTION IN NON-HOMOLOGOUS END JOINING DNA REPAIR.
[13]	"Cdc13 cooperates with the yeast Ku proteins and Stn1 to regulate telomerase recruitment." Grandin N., Damon C., Charbonneau M. Mol. Cell. Biol. 20:8397-8408(2000) [PubMed: 11046137] [Abstract] Cited for: FUNCTION IN TELOMERASE AND CDC13 TELOMERE RECRUITMENT.
[14]	"Involvement of replicative polymerases, Tel1p, Mec1p, Cdc13p, and the Ku complex in telomere-telomere recombination." Tsai Y.-L., Tseng S.-F., Chang S.-H., Lin C.-C., Teng S.-C. Mol. Cell. Biol. 22:5679-5687(2002) [PubMed: 12138180] [Abstract] Cited for: FUNCTION IN TELOMERE RECOMBINATION.
[15]	"Ku interacts with telomerase RNA to promote telomere addition at native and broken chromosome ends." Stellwagen A.E., Haimberger Z.W., Veatch J.R., Gottschling D.E. Genes Dev. 17:2384-2395(2003) [PubMed: 12975323] [Abstract] Cited for: FUNCTION IN TELOMERIC REPAIR AND BINDING TO TLC1 STEM LOOP.
[16]	"The Ku heterodimer performs separable activities at double-strand breaks and chromosome termini." Bertuch A.A., Lundblad V. Mol. Cell. Biol. 23:8202-8215(2003) [PubMed: 14585978] [Abstract] Cited for: FUNCTION IN DOUBLE-STRAND DNA REPAIR AND TELOMERE MAINTENANCE.
[17]	"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].
[18]	"Separation-of-function mutants of yeast Ku80 reveal a Yku80p-Sir4p interaction involved in telomeric silencing." Roy R., Meier B., McAinsh A.D., Feldmann H.M., Jackson S.P. J. Biol. Chem. 279:86-94(2004) [PubMed: 14551211] [Abstract] Cited for: FUNCTION IN TELOMERIC SILENCING, INTERACTION WITH SIR4.
[19]	"The DNA repair protein yKu80 regulates the function of recombination enhancer during yeast mating type switching." Ruan C., Workman J.L., Simpson R.T. Mol. Cell. Biol. 25:8476-8485(2005) [PubMed: 16166630] [Abstract] Cited for: FUNCTION IN MATING-TYPE SWITCHING.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AM296333 Genomic DNA. Translation: CAL35984.1. AM296334 Genomic DNA. Translation: CAL35983.1. AM296335 Genomic DNA. Translation: CAL35982.1. AM296336 Genomic DNA. Translation: CAL35981.1. AM296337 Genomic DNA. Translation: CAL35980.1. AM296338 Genomic DNA. Translation: CAL35979.1. AM296339 Genomic DNA. Translation: CAL35978.1. AM296340 Genomic DNA. Translation: CAL35977.1. AM296341 Genomic DNA. Translation: CAL35976.1. AM296342 Genomic DNA. Translation: CAL35975.1. AM296343 Genomic DNA. Translation: CAL35974.1. AM296344 Genomic DNA. Translation: CAL35973.1. AM296345 Genomic DNA. Translation: CAL35972.1. Z49702 Genomic DNA. Translation: CAA89742.1. BK006946 Genomic DNA. Translation: DAA10003.1.
PIR	S54567.
RefSeq	NP_013824.1. NM_001182606.1.
3D structure databases
ProteinModelPortal	Q04437.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2757N.
IntAct	Q04437. 66 interactions.
MINT	MINT-619682.
STRING	Q04437.
Proteomic databases
PeptideAtlas	Q04437.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YMR106C; YMR106C; YMR106C.
GeneID	855132.
KEGG	sce:YMR106C.
NMPDR	fig|4932.3.peg.4872.
Organism-specific databases
CYGD	YMR106c.
SGD	S000004712. YKU80.
Phylogenomic databases
eggNOG	fuNOG07029.
GeneTree	EFGT00050000006722.
HOGENOM	HBG203427.
OMA	YRYGADY.
OrthoDB	EOG4897WC.
Gene expression databases
ArrayExpress	Q04437.
Genevestigator	Q04437.
GermOnline	YMR106C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR006164. DNA_helicase_ATP-dep_Ku. IPR024193. DNA_helicase_ATP-dep_Ku80. IPR005160. Ku_C. IPR005161. Ku_N. IPR016194. SPOC-like. [Graphical view]
Gene3D	G3DSA:2.40.290.10. G3DSA:2.40.290.10. 1 hit.
KO	K10885.
Pfam	PF02735. Ku. 1 hit. PF03730. Ku_C. 1 hit. PF03731. Ku_N. 1 hit. [Graphical view]
PIRSF	PIRSF016570. Ku80. 1 hit.
SMART	SM00559. Ku78. 1 hit. [Graphical view]
SUPFAM	SSF100939. SPOC-like. 1 hit.
ProtoNet	Search...
Other
NextBio	978505.

Entry information

Entry name

KU80_YEAST

Accession

Primary (citable) accession number: Q04437
Secondary accession number(s): D6VZS9 , Q0P737, Q0P738, Q0P741, Q0P749

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	December 14, 2011
This is version 99 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program