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Protein

Flap endonuclease 1

Gene

rad2

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission 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 annotation

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 bindingi159 – 1591Magnesium 1UniRule annotation
Binding sitei159 – 1591DNA substrateUniRule annotation
Metal bindingi161 – 1611Magnesium 1UniRule annotation
Metal bindingi180 – 1801Magnesium 2UniRule annotation
Metal bindingi182 – 1821Magnesium 2UniRule annotation
Binding sitei232 – 2321DNA substrateUniRule annotation
Metal bindingi234 – 2341Magnesium 2UniRule annotation
Binding sitei234 – 2341DNA substrateUniRule annotation

GO - Molecular functioni

  • 5'-3' exodeoxyribonuclease activity involved in UV-damage excision repair Source: PomBase
  • 5'-flap endonuclease activity Source: PomBase
  • DNA binding Source: InterPro
  • double-stranded DNA 5'-3' exodeoxyribonuclease activity Source: PomBase
  • metal ion binding Source: UniProtKB-KW
  • single-stranded DNA 5'-3' exodeoxyribonuclease activity Source: PomBase

GO - Biological processi

  • DNA synthesis involved in DNA repair Source: PomBase
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
  • removal of RNA primer involved in mitotic DNA replication Source: PomBase
  • UV-damage excision repair Source: GOC
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

ReactomeiR-SPO-174437. Removal of the Flap Intermediate from the C-strand.
R-SPO-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SPO-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):
DNA repair protein rad2
Flap structure-specific endonuclease 1UniRule annotation
Gene namesi
Name:rad2UniRule annotation
Synonyms:fen1UniRule annotation
ORF Names:SPAC3G6.06c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC3G6.06c.
PomBaseiSPAC3G6.06c. rad2.

Subcellular locationi

  • Nucleusnucleolus UniRule annotation
  • Nucleusnucleoplasm UniRule annotation
  • Mitochondrion UniRule annotation

  • Note: Resides mostly in the nucleoli and relocalizes to the nucleoplasm upon DNA damage.UniRule annotation

GO - Cellular componenti

  • mitochondrion Source: UniProtKB-SubCell
  • nuclear replication fork Source: PomBase
  • nucleolus Source: UniProtKB-SubCell
  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: PomBase
  • site of double-strand break Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 380380Flap endonuclease 1PRO_0000154037Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei350 – 3501Phosphoserine1 Publication
Modified residuei351 – 3511Phosphoserine1 Publication

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP39750.

PTM databases

iPTMnetiP39750.

Interactioni

Subunit structurei

Interacts with PCNA. Three molecules of rad2 bind to one PCNA trimer with each molecule binding to one PCNA monomer. PCNA stimulates the nuclease activity without altering cleavage specificity.UniRule annotation

Protein-protein interaction databases

BioGridi279595. 100 interactions.
MINTiMINT-4689381.

Structurei

3D structure databases

ProteinModelPortaliP39750.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 105105N-domainAdd
BLAST
Regioni123 – 254132I-domainAdd
BLAST
Regioni337 – 3459Interaction with PCNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000193853.
InParanoidiP39750.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG7QK0MK.
PhylomeDBiP39750.

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.

P39750-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIKGLAQVL SEHAPASVKH NDIKNYFGRK VAIDASMSLY QFLIQVRSQD
60 70 80 90 100
GQQLMNEQGE TTSHLMGMFY RTLRIVDNGI KPCFVFDGKP PTLKSGELAK
110 120 130 140 150
RVARHQKARE DQEETKEVGT AEMVDRFAKR TVKVTRQHND EAKRLLELMG
160 170 180 190 200
IPFVNAPCEA EAQCAALARS GKVYAAASED MDTLCFQAPV LLRHLTFSEQ
210 220 230 240 250
RKEPISEYNI EKALNGLDMS VEQFVDLCIL LGCDYCEPIR GVGPARAVEL
260 270 280 290 300
IRQYGTLDRF VKEADRSKYP IPEDWPYEDA RRLFLDAEVL PGEEIELKWK
310 320 330 340 350
SPDADGIIQF LVKEKGFNED RVKLGINRLE KASKTIPQGR LDSFFKPVPS
360 370 380
SPKKPVDTKS KGSAKRKRDS NKGGESKKKR
Length:380
Mass (Da):42,866
Last modified:February 1, 1995 - v1
Checksum:i3604065D9B934CBF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77041 Genomic DNA. Translation: CAB36991.1.
CU329670 Genomic DNA. Translation: CAB16282.1.
PIRiA56054.
RefSeqiNP_594972.1. NM_001020403.2.

Genome annotation databases

EnsemblFungiiSPAC3G6.06c.1; SPAC3G6.06c.1:pep; SPAC3G6.06c.
GeneIDi2543164.
KEGGispo:SPAC3G6.06c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X77041 Genomic DNA. Translation: CAB36991.1.
CU329670 Genomic DNA. Translation: CAB16282.1.
PIRiA56054.
RefSeqiNP_594972.1. NM_001020403.2.

3D structure databases

ProteinModelPortaliP39750.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi279595. 100 interactions.
MINTiMINT-4689381.

PTM databases

iPTMnetiP39750.

Proteomic databases

MaxQBiP39750.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC3G6.06c.1; SPAC3G6.06c.1:pep; SPAC3G6.06c.
GeneIDi2543164.
KEGGispo:SPAC3G6.06c.

Organism-specific databases

EuPathDBiFungiDB:SPAC3G6.06c.
PomBaseiSPAC3G6.06c. rad2.

Phylogenomic databases

HOGENOMiHOG000193853.
InParanoidiP39750.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG7QK0MK.
PhylomeDBiP39750.

Enzyme and pathway databases

ReactomeiR-SPO-174437. Removal of the Flap Intermediate from the C-strand.
R-SPO-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SPO-69166. Removal of the Flap Intermediate.

Miscellaneous databases

PROiP39750.

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. "Structural and functional conservation of the human homolog of the Schizosaccharomyces pombe rad2 gene, which is required for chromosome segregation and recovery from DNA damage."
    Murray J.M., Tavassoli M., Al-Harithy R., Sheldrick K.S., Lehmann A.R., Carr A.M., Watts F.Z.
    Mol. Cell. Biol. 14:4878-4888(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-350 AND SER-351, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiFEN1_SCHPO
AccessioniPrimary (citable) accession number: P39750
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 8, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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.