ATP-dependent DNA helicase II subunit 2 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot Q04437 (KU80_YEAST)

Last modified January 19, 2010. Version 82. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    ATP-dependent DNA helicase II subunit 2
    EC=3.6.1.-
Alternative name(s):
    ATP-dependent DNA helicase II subunit Ku80
    Yeast Ku80
    High affinity DNA-binding factor subunit 2

Gene names

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

Organism

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

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

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Protein attributes

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

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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.3 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.17 Ref.18
Subunit structure	Heterodimer of YKU70/HDF1 and YKU80/HDF2. Interacts with SIR4. Ref.3 Ref.17 Ref.4
Subcellular location	Nucleus. Telomere Ref.7.
Miscellaneous	Present with 358 molecules/cell in log phase SD medium. Ref.16
Sequence similarities	Belongs to the ku80 family. Contains 1 Ku domain.

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Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair
Cellular component	Chromosomal protein Nucleus Telomere
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	chromatin assembly or disassembly Inferred from direct assay. Source: SGD chromatin silencing Inferred from direct assay. Source: SGD donor selection Ref.18 Inferred from direct assay. 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	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 Ref.14 Inferred from direct assay. Source: SGD damaged DNA binding Traceable author statement. Source: SGD protein binding Ref.17 Inferred from physical interaction. Source: IntAct telomeric DNA binding Inferred from direct assay. Source: SGD
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
SIR4	P11978	1	EBI-8224,EBI-17237
YKU70	P32807	1	EBI-8224,EBI-8214

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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

Natural variations

Natural variant

149

L → V in strain: DBVPG6044, SK1 and YPS128.

Natural variant

301

S → L in strain: DBVPG1853.

Natural variant

349

N → D in strain: DBVPG6044, SK1 and YPS128.

Natural variant

499

G → D in strain: DBVPG1853.

Natural variant

518

E → A in strain: DBVPG6044, SK1 and YPS128.

Natural variant

528

T → A in strain: DBVPG1853.

Natural variant

585

I → S in strain: DBVPG6763.

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Sequences

Sequence

Length

Mass (Da)

Tools

Q04437-1 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: 58126164EE375643
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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

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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. 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]	"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.
[4]	"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.
[5]	"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.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"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.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.
[15]	"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.
[16]	"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].
[17]	"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.
[18]	"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.

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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.
PIR	S54567.
RefSeq	NP_013824.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2757N.
IntAct	Q04437. 71 interactions.
STRING	Q04437.
Proteomic databases
PeptideAtlas	Q04437.
PRIDE	Q04437.
Genome annotation databases
Ensembl	YMR106C; YMR106C; YMR106C; Saccharomyces cerevisiae. [Genome view]
GeneID	855132.
KEGG	sce:YMR106C.
NMPDR	fig\|4932.3.peg.4872.
Organism-specific databases
CYGD	YMR106c.
SGD	S000004712. YKU80.
Phylogenomic databases
eggNOG	fuNOG07029.
HOGENOM	HBG203427.
OMA	YRYGADY.
OrthoDB	EOG91VMKD.
PhylomeDB	Q04437.
Gene expression databases
ArrayExpress	Q04437.
Genevestigator	Q04437.
GermOnline	YMR106C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR006164. DNA_helicase_ATP-dep_Ku. IPR005160. Ku_C. IPR005161. Ku_N. IPR016194. SPOC-like. [Graphical view]
Pfam	PF02735. Ku. 1 hit. PF03730. Ku_C. 1 hit. PF03731. Ku_N. 1 hit. [Graphical view]
SMART	SM00559. Ku78. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	978505.

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Entry information

Entry name

KU80_YEAST

Accession

Primary (citable) accession number: Q04437
Secondary accession number(s): Q0P737

Q0P749

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	January 19, 2010
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

SIMILARITY comments

Index of protein domains and families

Yeast

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

Yeast chromosome XIII

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

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents