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Protein

Flap endonuclease 1-A

Gene

fen1-a

Organism
Xenopus laevis (African clawed frog)
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 annotation2 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 annotationBy similarity
Binding sitei70 – 701DNA substrateUniRule annotationBy similarity
Metal bindingi86 – 861Magnesium 1UniRule annotation
Metal bindingi158 – 1581Magnesium 1UniRule annotation
Binding sitei158 – 1581DNA substrateUniRule annotationBy similarity
Metal bindingi160 – 1601Magnesium 1UniRule annotation
Metal bindingi179 – 1791Magnesium 2UniRule annotation
Metal bindingi181 – 1811Magnesium 2UniRule annotation
Binding sitei231 – 2311DNA substrateUniRule annotationBy similarity
Metal bindingi233 – 2331Magnesium 2UniRule annotation
Binding sitei233 – 2331DNA substrateUniRule annotationBy similarity

GO - Molecular functioni

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

GO - Biological processi

  • base-excision repair Source: UniProtKB
  • DNA replication Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Flap endonuclease 1-AUniRule annotation (EC:3.1.-.-UniRule annotation)
Short name:
FEN-1-AUniRule annotation
Alternative name(s):
Flap structure-specific endonuclease 1-AUniRule annotation
Short name:
xFEN-1a
Gene namesi
Name:fen1-a
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-955523. fen1.

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

Keywords - Cellular componenti

Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 382382Flap endonuclease 1-APRO_0000244491Add
BLAST

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP70040.

Expressioni

Developmental stagei

First expressed at a low level in stage II oocytes. Expression increases dramatically from oocyte stages III to V (at protein level). Also expressed in embryos.1 Publication

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

BioGridi98905. 1 interaction.
IntActiP70040. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliP70040.
SMRiP70040. Positions 2-356.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 104104N-domainSequence analysisAdd
BLAST
Regioni122 – 253132I-domainSequence analysisAdd
BLAST
Regioni336 – 3449Interaction with PCNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG000844.
KOiK04799.

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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P70040-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIHGLAKLI ADVAPAAIKE HDIKSYFGRK VAVDASMCIY QFLIAVRQDG
60 70 80 90 100
NTLQNEEGET TSHLMGMFYR TIRMVEHGIK PVYVFDGKPP QMKSGELAKR
110 120 130 140 150
SERRAEAEKL LEAAEEAGEV ENIEKFTKRL VKVTKQHNEE CKKLLTLMGI
160 170 180 190 200
PYVDAPCEAE ATCAALVKAG KVYAAATEDM DALTFGTPVL LRHLTASEAK
210 220 230 240 250
KLPIQEFHLN RVIQDIGITH EQFVDLCILL GSDYCETIRG IGPKRAIDLI
260 270 280 290 300
RQHKTIDEII DNIDLKKYPV PENWLHKEAK HLFLEPEVVD TDITELKWIE
310 320 330 340 350
PDEEGLVAFM CGEKQFSEDR IRNGAKKLAK NRQGSTQGRL DDFFKVTGSV
360 370 380
SSTKRKEAES KGSAKKKAKT GGTPAGKFKR GK
Length:382
Mass (Da):42,668
Last modified:February 1, 1997 - v1
Checksum:i9B1DB0EDAD158D57
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti33 – 331V → I in allele fen-1a'. 3 Publications

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF036327 mRNA. Translation: AAB88707.1.
U64563 mRNA. Translation: AAB06176.1.
AF065397 mRNA. Translation: AAD02814.1.
BC169761 mRNA. Translation: AAI69761.1.
BC169765 mRNA. Translation: AAI69765.1.
BC124977 mRNA. Translation: AAI24978.1.
RefSeqiNP_001080960.1. NM_001087491.1.
UniGeneiXl.440.

Genome annotation databases

GeneIDi394303.
KEGGixla:394303.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF036327 mRNA. Translation: AAB88707.1.
U64563 mRNA. Translation: AAB06176.1.
AF065397 mRNA. Translation: AAD02814.1.
BC169761 mRNA. Translation: AAI69761.1.
BC169765 mRNA. Translation: AAI69765.1.
BC124977 mRNA. Translation: AAI24978.1.
RefSeqiNP_001080960.1. NM_001087491.1.
UniGeneiXl.440.

3D structure databases

ProteinModelPortaliP70040.
SMRiP70040. Positions 2-356.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi98905. 1 interaction.
IntActiP70040. 1 interaction.

Proteomic databases

PRIDEiP70040.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi394303.
KEGGixla:394303.

Organism-specific databases

CTDi394303.
XenbaseiXB-GENE-955523. fen1.

Phylogenomic databases

HOVERGENiHBG000844.
KOiK04799.

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.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Involvement of flap endonuclease 1 in base excision DNA repair."
    Kim K., Biade S., Matsumoto Y.
    J. Biol. Chem. 273:8842-8848(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, IDENTIFICATION IN A COMPLEX WITH PCNA, VARIANT ILE-33.
    Tissue: Oocyte1 Publication.
  2. "Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism."
    Bibikova M., Wu B., Chi E., Kim K.-H., Trautman J.K., Carroll D.
    J. Biol. Chem. 273:34222-34229(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, COFACTOR, IDENTIFICATION IN A COMPLEX WITH PCNA, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, VARIANT ILE-33.
    Tissue: Tadpole head1 Publication.
  3. "Cloning and investigation of Xenopus Fen1: developmental expression and function in DNA replication."
    Li J.-L., Cox L.S.
    Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. NIH - Xenopus Gene Collection (XGC) project
    Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ILE-33.
    Tissue: Oocyte and Ovary.

Entry informationi

Entry nameiFEN1A_XENLA
AccessioniPrimary (citable) accession number: P70040
Secondary accession number(s): B7ZQC8, O57351, Q08AW7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: February 1, 1997
Last modified: November 11, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Documents

  1. 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.