Reviewed, UniProtKB/Swiss-Prot P07271 (PIF1_YEAST)

Names and origin

Protein names

Recommended name:
    DNA repair and recombination protein PIF1
    EC=3.6.1.-
Alternative name(s):
    ATP-dependent helicase PIF1
    Telomere stability protein 1

Gene names

Name:	PIF1
Synonyms:	TST1
Ordered Locus Names:	YML061C
ORF Names:	YM9958.01C

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	859 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of genomic stability. Involved in the maintenance of mitochondrial (mtDNA), ribosomal (rDNA) and telomeric DNA, and may also have a general role in chromosomal replication by affecting Okazaki fragment maturation. Inhibits telomere elongation and de novo telomere formation via catalytic inhibition of telomerase. Reduces the processivity of telomerase by displacing active telomerase from DNA ends. Releases telomerase by unwinding the short telomerase RNA/telomeric DNA hybrid that is the intermediate in the telomerase reaction. Required to maintain mtDNA under conditions that introduce dsDNA breaks in mtDNA, either preventing or repairing dsDNA breaks. May inhibit replication progression to allow time for repair. Required for efficient fork arrest at the replicaion fork barrier within rDNA. May have a role in conjunction with DNA2 helicase/nuclease in 5'-flap extension during Okazaki fragment processing. Ref.1 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18 Ref.19 Ref.20
Cofactor	Divalent cation ions.
Subunit structure	Monomer. Associates with mitochondrial and telomeric DNA. Binding to mtDNA is non-specific and the protein seems to coat the entire mtDNA molecule. Binds to the telomerase RNA TLC1. Ref.17 Ref.3
Subcellular location	Mitochondrion. Nucleus › nucleolus. Note: The nuclear isoform is mainly concentrated in the nucleolus, and occasionally redistributes to single nuclear foci outside the nucleolus, probably sites of DNA repair. Ref.15 Ref.4 Ref.11
Induction	Cell cycle-regulated. The nuclear isoform is present in very low amounts in G1 phase cells, but increases as cells progress through S phase, with a peak in late S/G2. The mitochondrial isoform follows a similar, but less pronounced induction pattern. The nuclear isoform is prone to APC/C-dependent degradation in G1, whereas the mitochondrial isoform is not. Ref.20
Miscellaneous	Present with 259 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the helicase family.
Biophysicochemical properties	Kinetic parameters: KM=1.3 mM for ATP KM=0.4 mM for dATP pH dependence: Optimum pH is 7.5-9.5.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair
Cellular component	Mitochondrion Nucleus
Coding sequence diversity	Alternative initiation
Domain	Transit peptide
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA recombination Ref.4 Inferred from mutant phenotype. Source: SGD DNA repair Inferred from electronic annotation. Source: UniProtKB-KW mitochondrial genome maintenance Ref.12 Inferred from mutant phenotype. Source: SGD negative regulation of telomere maintenance via telomerase Ref.14 Inferred from direct assay. Source: SGD telomere maintenance Ref.7 Inferred from mutant phenotype. Source: SGD
Cellular component	mitochondrion Ref.4 Ref.11 Inferred from direct assay. Source: SGD nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA helicase activity Ref.3 Inferred from direct assay. Source: SGD telomerase inhibitor activity Ref.14 Inferred from direct assay. Source: SGD
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Mitochondrial (identifier: P07271-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Nuclear (identifier: P07271-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-39: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 45	45	Mitochondrion
	Chain	46 – 859	814	DNA repair and recombination protein PIF1		PRO_0000013269
Regions
	Nucleotide binding	258 – 265	8	ATP Probable
	DNA binding	727 – 746	20	Potential
Amino acid modifications
	Modified residue	47	1	Phosphoserine Ref.22
	Modified residue	169	1	Phosphoserine Ref.22 Ref.21
	Modified residue	170	1	Phosphoserine Ref.22
	Modified residue	210	1	Phosphoserine Ref.21
	Modified residue	584	1	Phosphoserine Ref.22
Natural variations
	Alternative sequence	1 – 39	39	Missing in isoform Nuclear.		VSP_034601
Experimental info
	Mutagenesis	1	1	M → A in PIF1-m1; loss of mitochondrial function. Ref.5
	Mutagenesis	40	1	M → A in PIF1-m2; loss of nuclear function. Ref.5
	Mutagenesis	264	1	K → A or R: Abolishes helicase activity resulting in elongated telomeres; binds normally to DNA substrates. Ref.7 Ref.14 Ref.15
	Sequence conflict	309	1	Missing in CAA28953. Ref.1
	Sequence conflict	322	1	V → VG in CAA28953. Ref.1
	Sequence conflict	426	1	D → E in CAA28953. Ref.1
	Sequence conflict	800 – 801	2	Missing in CAA28953. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Mitochondrial [UniParc]. Last modified July 1, 2008. Version 2. Checksum: D7E4CAE499822C2C	FASTA	859	97,682
	10 20 30 40 50 60 MPKWIRSTLN HIIPRRPFIC SFNSFLLLKN VSHAKLSFSM SSRGFRSNNF IQAQLKHPSI 70 80 90 100 110 120 LSKEDLDLLS DSDDWEEPDC IQLETEKQEK KIITDIHKED PVDKKPMRDK NVMNFINKDS 130 140 150 160 170 180 PLSWNDMFKP SIIQPPQLIS ENSFDQSSQK KSRSTGFKNP LRPALKKESS FDELQNNSIS 190 200 210 220 230 240 QERSLEMINE NEKKKMQFGE KIAVLTQRPS FTELQNDQDD SNLNPHNGVK VKIPICLSKE 250 260 270 280 290 300 QESIIKLAEN GHNIFYTGSA GTGKSILLRE MIKVLKGIYG RENVAVTAST GLAACNIGGI 310 320 330 340 350 360 TIHSFAGIGL GKGDADKLYK KVRRSRKHLR RWENIGALVV DEISMLDAEL LDKLDFIARK 370 380 390 400 410 420 IRKNHQPFGG IQLIFCGDFF QLPPVSKDPN RPTKFAFESK AWKEGVKMTI MLQKVFRQRG 430 440 450 460 470 480 DVKFIDMLNR MRLGNIDDET EREFKKLSRP LPDDEIIPAE LYSTRMEVER ANNSRLSKLP 490 500 510 520 530 540 GQVHIFNAID GGALEDEELK ERLLQNFLAP KELHLKVGAQ VMMVKNLDAT LVNGSLGKVI 550 560 570 580 590 600 EFMDPETYFC YEALTNDPSM PPEKLETWAE NPSKLKAAME REQSDGEESA VASRKSSVKE 610 620 630 640 650 660 GFAKSDIGEP VSPLDSSVFD FMKRVKTDDE VVLENIKRKE QLMQTIHQNS AGKRRLPLVR 670 680 690 700 710 720 FKASDMSTRM VLVEPEDWAI EDENEKPLVS RVQLPLMLAW SLSIHKSQGQ TLPKVKVDLR 730 740 750 760 770 780 RVFEKGQAYV ALSRAVSREG LQVLNFDRTR IKAHQKVIDF YLTLSSAESA YKQLEADEQV 790 800 810 820 830 840 KKRKLDYAPG PKYKAKSKSK SNSPAPISAT TQSNNGIAAM LQRHSRKRFQ LKKESNSNQV 850 HSLVSDEPRG QDTEDHILE
	Isoform Nuclear. Checksum: EF75E0595E9150DC	FASTA	820	93,099
	10 20 30 40 50 60 MSSRGFRSNN FIQAQLKHPS ILSKEDLDLL SDSDDWEEPD CIQLETEKQE KKIITDIHKE 70 80 90 100 110 120 DPVDKKPMRD KNVMNFINKD SPLSWNDMFK PSIIQPPQLI SENSFDQSSQ KKSRSTGFKN 130 140 150 160 170 180 PLRPALKKES SFDELQNNSI SQERSLEMIN ENEKKKMQFG EKIAVLTQRP SFTELQNDQD 190 200 210 220 230 240 DSNLNPHNGV KVKIPICLSK EQESIIKLAE NGHNIFYTGS AGTGKSILLR EMIKVLKGIY 250 260 270 280 290 300 GRENVAVTAS TGLAACNIGG ITIHSFAGIG LGKGDADKLY KKVRRSRKHL RRWENIGALV 310 320 330 340 350 360 VDEISMLDAE LLDKLDFIAR KIRKNHQPFG GIQLIFCGDF FQLPPVSKDP NRPTKFAFES 370 380 390 400 410 420 KAWKEGVKMT IMLQKVFRQR GDVKFIDMLN RMRLGNIDDE TEREFKKLSR PLPDDEIIPA 430 440 450 460 470 480 ELYSTRMEVE RANNSRLSKL PGQVHIFNAI DGGALEDEEL KERLLQNFLA PKELHLKVGA 490 500 510 520 530 540 QVMMVKNLDA TLVNGSLGKV IEFMDPETYF CYEALTNDPS MPPEKLETWA ENPSKLKAAM 550 560 570 580 590 600 EREQSDGEES AVASRKSSVK EGFAKSDIGE PVSPLDSSVF DFMKRVKTDD EVVLENIKRK 610 620 630 640 650 660 EQLMQTIHQN SAGKRRLPLV RFKASDMSTR MVLVEPEDWA IEDENEKPLV SRVQLPLMLA 670 680 690 700 710 720 WSLSIHKSQG QTLPKVKVDL RRVFEKGQAY VALSRAVSRE GLQVLNFDRT RIKAHQKVID 730 740 750 760 770 780 FYLTLSSAES AYKQLEADEQ VKKRKLDYAP GPKYKAKSKS KSNSPAPISA TTQSNNGIAA 790 800 810 820 MLQRHSRKRF QLKKESNSNQ VHSLVSDEPR GQDTEDHILE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the PIF gene involved in repair and recombination of yeast mitochondrial DNA." Foury F., Lahaye A. EMBO J. 6:1441-1449(1987) [PubMed: 3038524] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN MITOCHONDRIAL DNA REPAIR.
[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]	"PIF1 DNA helicase from Saccharomyces cerevisiae. Biochemical characterization of the enzyme." Lahaye A., Leterme S., Foury F. J. Biol. Chem. 268:26155-26161(1993) [PubMed: 8253734] [Abstract] Cited for: PROTEIN SEQUENCE OF N-TERMINUS, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
[4]	"PIF1: a DNA helicase in yeast mitochondria." Lahaye A., Stahl H., Thines-Sempoux D., Foury F. EMBO J. 10:997-1007(1991) [PubMed: 1849081] [Abstract] Cited for: CHARACTERIZATION, SUBCELLULAR LOCATION.
[5]	"The Saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation." Schulz V.P., Zakian V.A. Cell 76:145-155(1994) [PubMed: 8287473] [Abstract] Cited for: FUNCTION IN TELOMERE LENGTH REGULATION, MUTAGENESIS OF MET-1 AND MET-40, ALTERNATIVE PRODUCT.
[6]	"The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA." Ivessa A.S., Zhou J.-Q., Zakian V.A. Cell 100:479-489(2000) [PubMed: 10693764] [Abstract] Cited for: FUNCTION IN RIBOSOMAL DNA MAINTENANCE.
[7]	"Pif1p helicase, a catalytic inhibitor of telomerase in yeast." Zhou J.-Q., Monson E.K., Teng S.-C., Schulz V.P., Zakian V.A. Science 289:771-774(2000) [PubMed: 10926538] [Abstract] Cited for: FUNCTION IN TELOMERE LENGTH REGULATION, MUTAGENESIS OF LYS-264.
[8]	"Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae." Myung K., Chen C., Kolodner R.D. Nature 411:1073-1076(2001) [PubMed: 11429610] [Abstract] Cited for: FUNCTION IN GENOMIC DNA MAINTENANCE.
[9]	"Mitochondrial dysfunction due to oxidative mitochondrial DNA damage is reduced through cooperative actions of diverse proteins." O'Rourke T.W., Doudican N.A., Mackereth M.D., Doetsch P.W., Shadel G.S. Mol. Cell. Biol. 22:4086-4093(2002) [PubMed: 12024022] [Abstract] Cited for: FUNCTION IN MITOCHONDRIAL DNA REPAIR.
[10]	"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].
[11]	"The proteome of Saccharomyces cerevisiae mitochondria." Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E., Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P., Pfanner N., Meisinger C. Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003) [PubMed: 14576278] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[12]	"Differential involvement of the related DNA helicases Pif1p and Rrm3p in mtDNA point mutagenesis and stability." O'Rourke T.W., Doudican N.A., Zhang H., Eaton J.S., Doetsch P.W., Shadel G.S. Gene 354:86-92(2005) [PubMed: 15907372] [Abstract] Cited for: FUNCTION IN MITOCHONDRIAL DNA REPAIR.
[13]	"Oxidative DNA damage causes mitochondrial genomic instability in Saccharomyces cerevisiae." Doudican N.A., Song B., Shadel G.S., Doetsch P.W. Mol. Cell. Biol. 25:5196-5204(2005) [PubMed: 15923634] [Abstract] Cited for: FUNCTION IN MITOCHONDRIAL DNA REPAIR.
[14]	"The yeast Pif1p helicase removes telomerase from telomeric DNA." Boule J.-B., Vega L.R., Zakian V.A. Nature 438:57-61(2005) [PubMed: 16121131] [Abstract] Cited for: FUNCTION IN TELOMERE LENGTH REGULATION, MUTAGENESIS OF LYS-264.
[15]	"The absence of Top3 reveals an interaction between the Sgs1 and Pif1 DNA helicases in Saccharomyces cerevisiae." Wagner M., Price G., Rothstein R. Genetics 174:555-573(2006) [PubMed: 16816432] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LYS-264, SUBCELLULAR LOCATION.
[16]	"Evidence suggesting that Pif1 helicase functions in DNA replication with the Dna2 helicase/nuclease and DNA polymerase delta." Budd M.E., Reis C.C., Smith S., Myung K., Campbell J.L. Mol. Cell. Biol. 26:2490-2500(2006) [PubMed: 16537895] [Abstract] Cited for: FUNCTION IN DNA REPLICATION.
[17]	"The finger subdomain of yeast telomerase cooperates with Pif1p to limit telomere elongation." Eugster A., Lanzuolo C., Bonneton M., Luciano P., Pollice A., Pulitzer J.F., Stegberg E., Berthiau A.-S., Foerstemann K., Corda Y., Lingner J., Geli V., Gilson E. Nat. Struct. Mol. Biol. 13:734-739(2006) [PubMed: 16878131] [Abstract] Cited for: FUNCTION IN TELOMERE LENGTH REGULATION, INTERACTION WITH TELOMERASE RNA.
[18]	"The role of Pif1p, a DNA helicase in Saccharomyces cerevisiae, in maintaining mitochondrial DNA." Cheng X., Dunaway S., Ivessa A.S. Mitochondrion 7:211-222(2007) [PubMed: 17257907] [Abstract] Cited for: FUNCTION IN MITOCHONDRIAL DNA MAINTENANCE, DNA BINDING.
[19]	"The yeast Pif1p DNA helicase preferentially unwinds RNA-DNA substrates." Boule J.-B., Zakian V.A. Nucleic Acids Res. 35:5809-5818(2007) [PubMed: 17720711] [Abstract] Cited for: FUNCTION.
[20]	"Sensitivity of yeast strains with long G-tails to levels of telomere-bound telomerase." Vega L.R., Phillips J.A., Thornton B.R., Benanti J.A., Onigbanjo M.T., Toczyski D.P., Zakian V.A. PLoS Genet. 3:1065-1075(2007) [PubMed: 17590086] [Abstract] Cited for: FUNCTION IN TELOMERE LENGTH REGULATION, INDUCTION.
[21]	"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-169 AND SER-210, MASS SPECTROMETRY.
[22]	"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-47; SER-169; SER-170 AND SER-584, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X05342 Genomic DNA. Translation: CAA28953.1. Z46729 Genomic DNA. Translation: CAA86714.1. Z38114 Genomic DNA. Translation: CAA86260.1.
PIR	A29457.
RefSeq	NP_013650.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4448N.
IntAct	P07271. 3 interactions.
STRING	P07271.
Genome annotation databases
Ensembl	YML061C; YML061C; YML061C; Saccharomyces cerevisiae. [Genome view]
GeneID	854941.
KEGG	sce:YML061C.
Organism-specific databases
CYGD	YML061c.
SGD	S000004526. PIF1.
Phylogenomic databases
HOGENOM	HBG398055.
OMA	IFYTGSA.
OrthoDB	EOG9G4J6J.
Gene expression databases
ArrayExpress	P07271.
Genevestigator	P07271.
GermOnline	YML061C. Saccharomyces cerevisiae.
Family and domain databases
ProtoNet	Search...
Other Resources
NextBio	977992.

Entry information

Entry name

PIF1_YEAST

Accession

Primary (citable) accession number: P07271

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	July 1, 2008
Last modified:	December 15, 2009
This is version 88 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)