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Protein

Flap endonuclease 1

Gene

fen1

Organism
Xiphophorus maculatus (Southern platyfish) (Platypoecilus maculatus)
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 annotation1 Publication

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 sitei70 – 701DNA substrateUniRule annotation
Metal bindingi86 – 861Magnesium 1UniRule annotation
Metal bindingi158 – 1581Magnesium 1UniRule annotation
Binding sitei158 – 1581DNA substrateUniRule annotation
Metal bindingi160 – 1601Magnesium 1UniRule annotation
Metal bindingi179 – 1791Magnesium 2UniRule annotation
Metal bindingi181 – 1811Magnesium 2UniRule annotation
Binding sitei231 – 2311DNA substrateUniRule annotation
Metal bindingi233 – 2331Magnesium 2UniRule annotation
Binding sitei233 – 2331DNA 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

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:fen1
OrganismiXiphophorus maculatus (Southern platyfish) (Platypoecilus maculatus)
Taxonomic identifieri8083 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiNeoteleosteiAcanthomorphataOvalentariaAtherinomorphaeCyprinodontiformesPoeciliidaePoeciliinaeXiphophorus
Proteomesi
  • UP000002852 Componenti: Unassembled WGS sequence

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 – 380380Flap endonuclease 1PRO_0000403492Add
BLAST

Post-translational modificationi

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

Keywords - PTMi

Phosphoprotein

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

STRINGi8083.ENSXMAP00000006136.

Structurei

3D structure databases

ProteinModelPortaliQ5I4H3.
SMRiQ5I4H3. Positions 2-356.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG2519. Eukaryota.
COG0258. LUCA.
GeneTreeiENSGT00640000091478.
HOVERGENiHBG000844.
InParanoidiQ5I4H3.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG72JWHG.

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.
PS00842. XPG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5I4H3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGIHGLAKLI ADHAPGAIKE QDIKNYFGRK IAIDASMCIY QFLIAVRQDG
60 70 80 90 100
NVLQSEDGET TSHLMGMFYR TIRMLENGIK PVYVFDGKPP QLKSAELEKR
110 120 130 140 150
GERRAEAEKM LAKAQELGEQ ENIDKFSKRL VKVTKQHNDD CKKLLTLMGV
160 170 180 190 200
PYIEAPCEAE ASCAALVKEG KVFATATEDM DGLTFGTNVL LRHLTASEAK
210 220 230 240 250
KLPVQEFHFN RILQDIGLTS EQFIDLCILL GCDYCGTIKG IGPKRAIDLI
260 270 280 290 300
RQHGSIEEIL ENIDTSKHPA PEDWLYKEAR NLFLKPEVVD SSTVDLKWRE
310 320 330 340 350
PDEEALIQFM CSEKQFSEDR IRNGCKKMMK SRQGSTQGRL DSFFSVTGSL
360 370 380
SSKRKEPETK GSAKKKQKTG ATPGKFRKGK
Length:380
Mass (Da):42,652
Last modified:February 15, 2005 - v1
Checksum:i5017F56E64D0AB7D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY855347 mRNA. Translation: AAW55636.1.
AY855348 Genomic DNA. Translation: AAW55637.1.
RefSeqiNP_001273228.1. NM_001286299.1.
XP_014325945.1. XM_014470459.1.

Genome annotation databases

EnsembliENSXMAT00000006142; ENSXMAP00000006136; ENSXMAG00000006103.
GeneIDi102228373.
KEGGixma:102228373.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY855347 mRNA. Translation: AAW55636.1.
AY855348 Genomic DNA. Translation: AAW55637.1.
RefSeqiNP_001273228.1. NM_001286299.1.
XP_014325945.1. XM_014470459.1.

3D structure databases

ProteinModelPortaliQ5I4H3.
SMRiQ5I4H3. Positions 2-356.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi8083.ENSXMAP00000006136.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSXMAT00000006142; ENSXMAP00000006136; ENSXMAG00000006103.
GeneIDi102228373.
KEGGixma:102228373.

Organism-specific databases

CTDi2237.

Phylogenomic databases

eggNOGiKOG2519. Eukaryota.
COG0258. LUCA.
GeneTreeiENSGT00640000091478.
HOVERGENiHBG000844.
InParanoidiQ5I4H3.
KOiK04799.
OMAiGSQDYDS.
OrthoDBiEOG72JWHG.

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.
PS00842. XPG_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Characterization and purification of flap endonuclease-1 (xiFEN-1) from Xiphophorus maculatus."
    Ruymgaart A.P., Heater S.J., Oehlers L.P. Jr., Rains J.D., Walter R.B.
    Zebrafish 1:273-285(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION.
    Strain: Jp 163 A.

Entry informationi

Entry nameiFEN1_XIPMA
AccessioniPrimary (citable) accession number: Q5I4H3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: February 15, 2005
Last modified: July 6, 2016
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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.