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Protein

Flap endonuclease 1

Gene

RAD27

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Structure-specific nuclease with 5'-flap endonuclease and 5'-3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site-terminated flap. Acts as a genome stabilization factor that prevents flaps from equilibrating into structurs that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA, and exhibits RNase H activity. Also involved in replication and repair of rDNA and in repairing mitochondrial DNA.UniRule annotation8 Publications

Cofactori

Mg2+UniRule annotationNote: Binds 2 magnesium ions per subunit. They probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi34 – 341Magnesium 1UniRule annotation
Binding sitei47 – 471DNA substrateUniRule annotation
Binding sitei71 – 711DNA substrateUniRule annotation
Metal bindingi87 – 871Magnesium 1UniRule annotation
Metal bindingi156 – 1561Magnesium 1UniRule annotation
Binding sitei156 – 1561DNA substrateUniRule annotation
Metal bindingi158 – 1581Magnesium 1UniRule annotation
Metal bindingi177 – 1771Magnesium 2UniRule annotation
Metal bindingi179 – 1791Magnesium 2UniRule annotation
Binding sitei229 – 2291DNA substrateUniRule annotation
Metal bindingi231 – 2311Magnesium 2UniRule annotation
Binding sitei231 – 2311DNA substrateUniRule annotation

GO - Molecular functioni

  • 5'-3' exonuclease activity Source: SGD
  • 5'-flap endonuclease activity Source: SGD
  • DNA binding Source: InterPro
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • base-excision repair, base-free sugar-phosphate removal Source: SGD
  • DNA replication, removal of RNA primer Source: SGD
  • double-strand break repair via nonhomologous end joining Source: SGD
  • gene conversion at mating-type locus, DNA repair synthesis Source: SGD
  • maintenance of DNA trinucleotide repeats Source: SGD
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
  • replicative cell aging Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31898-MONOMER.
ReactomeiR-SCE-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SCE-69166. Removal of the Flap Intermediate.

Names & Taxonomyi

Protein namesi
Recommended name:
Flap endonuclease 1UniRule annotation (EC:3.1.-.-UniRule annotation)
Short name:
FEN-1UniRule annotation
Alternative name(s):
Flap structure-specific endonuclease 1UniRule annotation
RAD2 homolog nuclease 1
Short name:
RTH1 nuclease
Structure-specific endonuclease RAD27
Gene namesi
Name:RAD27UniRule annotation
Synonyms:FEN1UniRule annotation, RTH1
Ordered Locus Names:YKL113C
ORF Names:YKL510
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKL113C.
SGDiS000001596. RAD27.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrion Source: SGD
  • nucleolus Source: UniProtKB-SubCell
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi67 – 671G → S: Deficient in double and single flap endonuclease cleavage and exonucleolytic cleavage. 1 Publication
Mutagenesisi176 – 1761E → A: Deficient in exonuclease and gap endonuclease activities, but retains almost all of its flap endonuclease activity. 1 Publication
Mutagenesisi240 – 2401G → D: Can only cleave double-flap structures with a 3' 1-nucleotide tail. Has no exonuclease activity. 1 Publication
Mutagenesisi346 – 3472FF → GA: Reduces interaction with POL30 more than 100 fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 382382Flap endonuclease 1PRO_0000154038Add
BLAST

Post-translational modificationi

Phosphorylated. Phosphorylation upon DNA damage induces relocalization to the nuclear plasma.UniRule annotation

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP26793.
PeptideAtlasiP26793.

PTM databases

iPTMnetiP26793.

Interactioni

Subunit structurei

Interacts with PCNA (POL30). Three molecules of RAD27 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
DNA2P388593EBI-14693,EBI-5973
POL30P158733EBI-14693,EBI-12993

Protein-protein interaction databases

BioGridi34021. 376 interactions.
DIPiDIP-2325N.
IntActiP26793. 3 interactions.
MINTiMINT-536469.

Structurei

3D structure databases

ProteinModelPortaliP26793.
SMRiP26793. Positions 2-333.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 105105N-domainAdd
BLAST
Regioni120 – 251132I-domainAdd
BLAST
Regioni339 – 3479Interaction with PCNAUniRule annotation

Sequence similaritiesi

Belongs to the XPG/RAD2 endonuclease family. FEN1 subfamily.UniRule annotation

Phylogenomic databases

GeneTreeiENSGT00640000091478.
InParanoidiP26793.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG7QK0MK.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR023426. Flap_endonuc.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR019974. XPG_CS.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PANTHERiPTHR11081. PTHR11081. 1 hit.
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF88723. SSF88723. 1 hit.
PROSITEiPS00841. XPG_1. 1 hit.
PS00842. XPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P26793-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIKGLNAII SEHVPSAIRK SDIKSFFGRK VAIDASMSLY QFLIAVRQQD
60 70 80 90 100
GGQLTNEAGE TTSHLMGMFY RTLRMIDNGI KPCYVFDGKP PDLKSHELTK
110 120 130 140 150
RSSRRVETEK KLAEATTELE KMKQERRLVK VSKEHNEEAQ KLLGLMGIPY
160 170 180 190 200
IIAPTEAEAQ CAELAKKGKV YAAASEDMDT LCYRTPFLLR HLTFSEAKKE
210 220 230 240 250
PIHEIDTELV LRGLDLTIEQ FVDLCIMLGC DYCESIRGVG PVTALKLIKT
260 270 280 290 300
HGSIEKIVEF IESGESNNTK WKIPEDWPYK QARMLFLDPE VIDGNEINLK
310 320 330 340 350
WSPPKEKELI EYLCDDKKFS EERVKSGISR LKKGLKSGIQ GRLDGFFQVV
360 370 380
PKTKEQLAAA AKRAQENKKL NKNKNKVTKG RR
Length:382
Mass (Da):43,279
Last modified:August 1, 1992 - v1
Checksum:i1F54B08720121C8C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S93804 Genomic DNA. Translation: AAB21998.1.
Z28113 Genomic DNA. Translation: CAA81953.1.
BK006944 Genomic DNA. Translation: DAA09045.1.
PIRiS22267.
RefSeqiNP_012809.1. NM_001179679.1.

Genome annotation databases

EnsemblFungiiYKL113C; YKL113C; YKL113C.
GeneIDi853747.
KEGGisce:YKL113C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S93804 Genomic DNA. Translation: AAB21998.1.
Z28113 Genomic DNA. Translation: CAA81953.1.
BK006944 Genomic DNA. Translation: DAA09045.1.
PIRiS22267.
RefSeqiNP_012809.1. NM_001179679.1.

3D structure databases

ProteinModelPortaliP26793.
SMRiP26793. Positions 2-333.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34021. 376 interactions.
DIPiDIP-2325N.
IntActiP26793. 3 interactions.
MINTiMINT-536469.

PTM databases

iPTMnetiP26793.

Proteomic databases

MaxQBiP26793.
PeptideAtlasiP26793.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL113C; YKL113C; YKL113C.
GeneIDi853747.
KEGGisce:YKL113C.

Organism-specific databases

EuPathDBiFungiDB:YKL113C.
SGDiS000001596. RAD27.

Phylogenomic databases

GeneTreeiENSGT00640000091478.
InParanoidiP26793.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG7QK0MK.

Enzyme and pathway databases

BioCyciYEAST:G3O-31898-MONOMER.
ReactomeiR-SCE-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SCE-69166. Removal of the Flap Intermediate.

Miscellaneous databases

PROiP26793.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR023426. Flap_endonuc.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
IPR006086. XPG-I_dom.
IPR006084. XPG/Rad2.
IPR019974. XPG_CS.
IPR006085. XPG_DNA_repair_N.
[Graphical view]
PANTHERiPTHR11081. PTHR11081. 1 hit.
PfamiPF00867. XPG_I. 1 hit.
PF00752. XPG_N. 1 hit.
[Graphical view]
PRINTSiPR00853. XPGRADSUPER.
SMARTiSM00279. HhH2. 1 hit.
SM00484. XPGI. 1 hit.
SM00485. XPGN. 1 hit.
[Graphical view]
SUPFAMiSSF47807. SSF47807. 1 hit.
SSF88723. SSF88723. 1 hit.
PROSITEiPS00841. XPG_1. 1 hit.
PS00842. XPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1 and the BAF1 loci and reveals one tRNA gene and several new open reading frames including homologs to RAD2 and kinases."
    Jacquier A., Legrain P., Dujon B.
    Yeast 8:121-132(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Purification and characterization of the DNA polymerase alpha associated exonuclease: the RTH1 gene product."
    Zhu F.X., Biswas E.E., Biswas S.B.
    Biochemistry 36:5947-5954(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 284-298, FUNCTION, EXONUCLEASE AND RNASE H ACTIVITIES.
  5. "Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair."
    Harrington J.J., Lieber M.R.
    Genes Dev. 8:1344-1355(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "Characterization of a mutant strain of Saccharomyces cerevisiae with a deletion of the RAD27 gene, a structural homolog of the RAD2 nucleotide excision repair gene."
    Reagan M.S., Pittenger C., Siede W., Friedberg E.C.
    J. Bacteriol. 177:364-371(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "Two modes of FEN1 binding to PCNA regulated by DNA."
    Gomes X.V., Burgers P.M.
    EMBO J. 19:3811-3821(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH POL30, MUTAGENESIS OF 346-PHE-PHE-347.
  8. "Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate."
    Kao H.I., Henricksen L.A., Liu Y., Bambara R.A.
    J. Biol. Chem. 277:14379-14389(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENDONUCLEASE ACTIVITY, SUBSTRATE SPECIFICITY, MUTAGENESIS OF GLY-240.
  9. "Okazaki fragment maturation in yeast. I. Distribution of functions between FEN1 AND DNA2."
    Ayyagari R., Gomes X.V., Gordenin D.A., Burgers P.M.
    J. Biol. Chem. 278:1618-1625(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "Reconstituted Okazaki fragment processing indicates two pathways of primer removal."
    Rossi M.L., Bambara R.A.
    J. Biol. Chem. 281:26051-26061(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF GLY-67.
  13. "Concerted action of exonuclease and Gap-dependent endonuclease activities of FEN-1 contributes to the resolution of triplet repeat sequences (CTG)n-and (GAA)n-derived secondary structures formed during maturation of Okazaki fragments."
    Singh P., Zheng L., Chavez V., Qiu J., Shen B.
    J. Biol. Chem. 282:3465-3477(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENDONUCLEASE AND EXONUCLEASE ACTIVITIES, MUTAGENESIS OF GLU-176.
  14. "Nucleolar localization and dynamic roles of flap endonuclease 1 in ribosomal DNA replication and damage repair."
    Guo Z., Qian L., Liu R., Dai H., Zhou M., Zheng L., Shen B.
    Mol. Cell. Biol. 28:4310-4319(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN RDNA REPLICATION AND REPAIR.
  15. "Evidence for a role of FEN1 in maintaining mitochondrial DNA integrity."
    Kalifa L., Beutner G., Phadnis N., Sheu S.S., Sia E.A.
    DNA Repair 8:1242-1249(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN MITOCHONDRIAL DNA REPAIR, SUBCELLULAR LOCATION.
  16. "The transition of closely opposed lesions to double-strand breaks during long-patch base excision repair is prevented by the coordinated action of DNA polymerase delta and Rad27/Fen1."
    Ma W., Panduri V., Sterling J.F., Van Houten B., Gordenin D.A., Resnick M.A.
    Mol. Cell. Biol. 29:1212-1221(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DNA REPAIR.
  17. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiFEN1_YEAST
AccessioniPrimary (citable) accession number: P26793
Secondary accession number(s): D6VXH5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: June 8, 2016
This is version 150 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 6120 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.