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Protein

Flap endonuclease 1

Gene

FEN1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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 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

GO - Biological processi

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

BioCyciARA:GQT-2791-MONOMER.
ARA:GQT-2794-MONOMER.
ReactomeiR-ATH-110362. POLB-Dependent Long Patch Base Excision Repair.
R-ATH-174437. Removal of the Flap Intermediate from the C-strand.
R-ATH-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-ATH-5685939. HDR through MMEJ (alt-NHEJ).
R-ATH-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
Gene namesi
Name:FEN1UniRule annotation
Ordered Locus Names:At5g26680
ORF Names:F21E10.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G26680.

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

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 383383Flap endonuclease 1PRO_0000403518Add
BLAST

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO65251.
PRIDEiO65251.

Expressioni

Gene expression databases

ExpressionAtlasiO65251. baseline and differential.

Interactioni

Subunit structurei

Interacts with PCNA. Three molecules of FEN1 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

STRINGi3702.AT5G26680.1.

Structurei

3D structure databases

ProteinModelPortaliO65251.
SMRiO65251. Positions 2-338.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 105105N-domainAdd
BLAST
Regioni123 – 254132I-domainAdd
BLAST
Regioni338 – 3469Interaction with PCNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG2519. Eukaryota.
COG0258. LUCA.
HOGENOMiHOG000193853.
InParanoidiO65251.
KOiK04799.
PhylomeDBiO65251.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
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.
SMARTiSM00475. 53EXOc. 1 hit.
SM00279. 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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: O65251-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MGIKGLTKLL ADNAPSCMKE QKFESYFGRK IAVDASMSIY QFLIVVGRTG
60 70 80 90 100
TEMLTNEAGE VTSHLQGMFN RTIRLLEAGI KPVYVFDGKP PELKRQELAK
110 120 130 140 150
RYSKRADATA DLTGAIEAGN KEDIEKYSKR TVKVTKQHND DCKRLLRLMG
160 170 180 190 200
VPVVEATSEA EAQCAALCKS GKVYGVASED MDSLTFGAPK FLRHLMDPSS
210 220 230 240 250
RKIPVMEFEV AKILEELQLT MDQFIDLCIL SGCDYCDSIR GIGGQTALKL
260 270 280 290 300
IRQHGSIETI LENLNKERYQ IPEEWPYNEA RKLFKEPDVI TDEEQLDIKW
310 320 330 340 350
TSPDEEGIVQ FLVNENGFNI DRVTKAIEKI KTAKNKSSQG RLESFFKPVA
360 370 380
NSSVPAKRKE IPESTTKGAA NKKTKGAGGR KKK
Length:383
Mass (Da):42,797
Last modified:January 11, 2011 - v2
Checksum:iD209B33E09B3A252
GO

Sequence cautioni

The sequence AAC13596.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF058914 Genomic DNA. Translation: AAC13596.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED93577.1.
PIRiT01198.
RefSeqiNP_001154740.1. NM_001161268.1. [O65251-1]
UniGeneiAt.47103.

Genome annotation databases

EnsemblPlantsiAT5G26680.2; AT5G26680.2; AT5G26680. [O65251-1]
GeneIDi832721.
KEGGiath:AT5G26680.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF058914 Genomic DNA. Translation: AAC13596.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED93577.1.
PIRiT01198.
RefSeqiNP_001154740.1. NM_001161268.1. [O65251-1]
UniGeneiAt.47103.

3D structure databases

ProteinModelPortaliO65251.
SMRiO65251. Positions 2-338.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G26680.1.

Proteomic databases

PaxDbiO65251.
PRIDEiO65251.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G26680.2; AT5G26680.2; AT5G26680. [O65251-1]
GeneIDi832721.
KEGGiath:AT5G26680.

Organism-specific databases

TAIRiAT5G26680.

Phylogenomic databases

eggNOGiKOG2519. Eukaryota.
COG0258. LUCA.
HOGENOMiHOG000193853.
InParanoidiO65251.
KOiK04799.
PhylomeDBiO65251.

Enzyme and pathway databases

BioCyciARA:GQT-2791-MONOMER.
ARA:GQT-2794-MONOMER.
ReactomeiR-ATH-110362. POLB-Dependent Long Patch Base Excision Repair.
R-ATH-174437. Removal of the Flap Intermediate from the C-strand.
R-ATH-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-ATH-5685939. HDR through MMEJ (alt-NHEJ).
R-ATH-69166. Removal of the Flap Intermediate.

Miscellaneous databases

PROiO65251.

Gene expression databases

ExpressionAtlasiO65251. baseline and differential.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00614. Fen.
InterProiIPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
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.
SMARTiSM00475. 53EXOc. 1 hit.
SM00279. 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.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
    Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
    , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
    Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.

Entry informationi

Entry nameiFEN1_ARATH
AccessioniPrimary (citable) accession number: O65251
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: January 11, 2011
Last modified: May 11, 2016
This is version 100 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: 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.