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Protein

Flap endonuclease 1

Gene

fen

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 3 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. Binds the unpaired 3'-DNA end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves one nucleotide into the double-stranded DNA from the junction in flap DNA, leaving a nick for ligation. Also involved in the base excision repair (BER) pathway. Acts as a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. Also possesses 5'-3' exonuclease activity on nicked or gapped double-stranded DNA (By similarity).By similarity

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 bindingi27 – 271Magnesium 1UniRule annotation
Metal bindingi80 – 801Magnesium 1UniRule annotation
Metal bindingi151 – 1511Magnesium 1UniRule annotation
Metal bindingi153 – 1531Magnesium 1UniRule annotation
Metal bindingi172 – 1721Magnesium 2UniRule annotation
Metal bindingi174 – 1741Magnesium 2UniRule annotation
Metal bindingi235 – 2351Magnesium 2UniRule 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

BioCyciAFUL224325:GJBC-272-MONOMER.
BRENDAi3.1.99.B1. 171.

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:fenUniRule annotation
Ordered Locus Names:AF_0264
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 336336Flap endonuclease 1PRO_0000154050Add
BLAST

Interactioni

Subunit structurei

Interacts with PCNA. PCNA stimulates the nuclease activity without altering cleavage specificity.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi224325.AF0264.

Structurei

Secondary structure

1
336
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 84Combined sources
Helixi16 – 194Combined sources
Beta strandi23 – 275Combined sources
Helixi28 – 3811Combined sources
Helixi56 – 7116Combined sources
Beta strandi74 – 796Combined sources
Helixi85 – 873Combined sources
Helixi88 – 11124Combined sources
Helixi116 – 1238Combined sources
Helixi128 – 14013Combined sources
Beta strandi145 – 1473Combined sources
Helixi152 – 16110Combined sources
Beta strandi164 – 1696Combined sources
Beta strandi171 – 1733Combined sources
Helixi174 – 1774Combined sources
Beta strandi181 – 1866Combined sources
Beta strandi207 – 2104Combined sources
Helixi211 – 2188Combined sources
Helixi222 – 23211Combined sources
Helixi245 – 25511Combined sources
Helixi258 – 2658Combined sources
Helixi273 – 2808Combined sources
Helixi297 – 3048Combined sources
Turni305 – 3084Combined sources
Helixi312 – 3198Combined sources
Helixi320 – 3223Combined sources
Beta strandi327 – 3293Combined sources
Helixi332 – 3343Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RXVX-ray2.50A/B1-336[»]
1RXWX-ray2.00A1-336[»]
1RXZX-ray2.00B326-336[»]
ProteinModelPortaliO29975.
SMRiO29975. Positions 4-323.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29975.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 9898N-domainAdd
BLAST
Regioni115 – 256142I-domainAdd
BLAST
Regioni328 – 3369Interaction with PCNA

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04050. Archaea.
COG0258. LUCA.
KOiK04799.
OMAiGSQDYDS.

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.
IPR019973. Flap_structure-sp_endonuc_arc.
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.
TIGRFAMsiTIGR03674. fen_arch. 1 hit.
PROSITEiPS00841. XPG_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29975-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGADIGDLFE REEVELEYFS GKKIAVDAFN TLYQFISIIR QPDGTPLKDS
60 70 80 90 100
QGRITSHLSG ILYRVSNMVE VGIRPVFVFD GEPPEFKKAE IEERKKRRAE
110 120 130 140 150
AEEMWIAALQ AGDKDAKKYA QAAGRVDEYI VDSAKTLLSY MGIPFVDAPS
160 170 180 190 200
EGEAQAAYMA AKGDVEYTGS QDYDSLLFGS PRLARNLAIT GKRKLPGKNV
210 220 230 240 250
YVDVKPEIII LESNLKRLGL TREQLIDIAI LVGTDYNEGV KGVGVKKALN
260 270 280 290 300
YIKTYGDIFR ALKALKVNID HVEEIRNFFL NPPVTDDYRI EFREPDFEKA
310 320 330
IEFLCEEHDF SRERVEKALE KLKALKSTQA TLERWF
Length:336
Mass (Da):38,065
Last modified:January 1, 1998 - v1
Checksum:i68778F204FD96F00
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90967.1.
PIRiH69282.
RefSeqiWP_010877775.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90967; AAB90967; AF_0264.
GeneIDi24793800.
KEGGiafu:AF_0264.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90967.1.
PIRiH69282.
RefSeqiWP_010877775.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RXVX-ray2.50A/B1-336[»]
1RXWX-ray2.00A1-336[»]
1RXZX-ray2.00B326-336[»]
ProteinModelPortaliO29975.
SMRiO29975. Positions 4-323.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0264.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90967; AAB90967; AF_0264.
GeneIDi24793800.
KEGGiafu:AF_0264.

Phylogenomic databases

eggNOGiarCOG04050. Archaea.
COG0258. LUCA.
KOiK04799.
OMAiGSQDYDS.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-272-MONOMER.
BRENDAi3.1.99.B1. 171.

Miscellaneous databases

EvolutionaryTraceiO29975.

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.
IPR019973. Flap_structure-sp_endonuc_arc.
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.
TIGRFAMsiTIGR03674. fen_arch. 1 hit.
PROSITEiPS00841. XPG_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair."
    Chapados B.R., Hosfield D.J., Han S., Qiu J., Yelent B., Shen B., Tainer J.A.
    Cell 116:39-50(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH DNA AND PCNA.

Entry informationi

Entry nameiFEN_ARCFU
AccessioniPrimary (citable) accession number: O29975
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: January 1, 1998
Last modified: May 11, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.