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FEN_NATPD
ID   FEN_NATPD               Reviewed;         328 AA.
AC   Q3IPG8;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   08-NOV-2005, sequence version 1.
DT   03-AUG-2022, entry version 99.
DE   RecName: Full=Flap endonuclease 1 {ECO:0000255|HAMAP-Rule:MF_00614};
DE            Short=FEN-1 {ECO:0000255|HAMAP-Rule:MF_00614};
DE            EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_00614};
DE   AltName: Full=Flap structure-specific endonuclease 1 {ECO:0000255|HAMAP-Rule:MF_00614};
GN   Name=fen {ECO:0000255|HAMAP-Rule:MF_00614}; OrderedLocusNames=NP_3784A;
OS   Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / JCM
OS   8858 / NBRC 14720 / NCIMB 2260 / Gabara) (Halobacterium pharaonis).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Halobacteriales;
OC   Haloarculaceae; Natronomonas.
OX   NCBI_TaxID=348780;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 35678 / DSM 2160 / CIP 103997 / JCM 8858 / NBRC 14720 / NCIMB
RC   2260 / Gabara;
RX   PubMed=16169924; DOI=10.1101/gr.3952905;
RA   Falb M., Pfeiffer F., Palm P., Rodewald K., Hickmann V., Tittor J.,
RA   Oesterhelt D.;
RT   "Living with two extremes: conclusions from the genome sequence of
RT   Natronomonas pharaonis.";
RL   Genome Res. 15:1336-1343(2005).
CC   -!- FUNCTION: Structure-specific nuclease with 5'-flap endonuclease and 5'-
CC       3' exonuclease activities involved in DNA replication and repair.
CC       During DNA replication, cleaves the 5'-overhanging flap structure that
CC       is generated by displacement synthesis when DNA polymerase encounters
CC       the 5'-end of a downstream Okazaki fragment. Binds the unpaired 3'-DNA
CC       end and kinks the DNA to facilitate 5' cleavage specificity. Cleaves
CC       one nucleotide into the double-stranded DNA from the junction in flap
CC       DNA, leaving a nick for ligation. Also involved in the base excision
CC       repair (BER) pathway. Acts as a genome stabilization factor that
CC       prevents flaps from equilibrating into structures that lead to
CC       duplications and deletions. Also possesses 5'-3' exonuclease activity
CC       on nicked or gapped double-stranded DNA (By similarity). {ECO:0000250}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00614};
CC       Note=Binds 2 magnesium ions per subunit. They probably participate in
CC       the reaction catalyzed by the enzyme. May bind an additional third
CC       magnesium ion after substrate binding. {ECO:0000255|HAMAP-
CC       Rule:MF_00614};
CC   -!- SUBUNIT: Interacts with PCNA. PCNA stimulates the nuclease activity
CC       without altering cleavage specificity. {ECO:0000255|HAMAP-
CC       Rule:MF_00614}.
CC   -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_00614}.
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DR   EMBL; CR936257; CAI49983.1; -; Genomic_DNA.
DR   RefSeq; WP_011323600.1; NC_007426.1.
DR   AlphaFoldDB; Q3IPG8; -.
DR   SMR; Q3IPG8; -.
DR   STRING; 348780.NP_3784A; -.
DR   EnsemblBacteria; CAI49983; CAI49983; NP_3784A.
DR   GeneID; 3702700; -.
DR   KEGG; nph:NP_3784A; -.
DR   eggNOG; arCOG04050; Archaea.
DR   HOGENOM; CLU_032444_0_0_2; -.
DR   OMA; GSQDYDS; -.
DR   OrthoDB; 41214at2157; -.
DR   Proteomes; UP000002698; Chromosome.
DR   GO; GO:0008409; F:5'-3' exonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0017108; F:5'-flap endonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0043137; P:DNA replication, removal of RNA primer; IEA:UniProtKB-UniRule.
DR   HAMAP; MF_00614; Fen; 1.
DR   InterPro; IPR036279; 5-3_exonuclease_C_sf.
DR   InterPro; IPR023426; Flap_endonuc.
DR   InterPro; IPR019973; Flap_structure-sp_endonuc_arc.
DR   InterPro; IPR008918; HhH2.
DR   InterPro; IPR029060; PIN-like_dom_sf.
DR   InterPro; IPR006086; XPG-I_dom.
DR   InterPro; IPR006084; XPG/Rad2.
DR   InterPro; IPR019974; XPG_CS.
DR   InterPro; IPR006085; XPG_DNA_repair_N.
DR   PANTHER; PTHR11081; PTHR11081; 1.
DR   Pfam; PF00867; XPG_I; 1.
DR   Pfam; PF00752; XPG_N; 1.
DR   PRINTS; PR00853; XPGRADSUPER.
DR   SMART; SM00279; HhH2; 1.
DR   SMART; SM00484; XPGI; 1.
DR   SMART; SM00485; XPGN; 1.
DR   SUPFAM; SSF47807; SSF47807; 1.
DR   SUPFAM; SSF88723; SSF88723; 1.
DR   TIGRFAMs; TIGR03674; fen_arch; 1.
DR   PROSITE; PS00841; XPG_1; 1.
PE   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Endonuclease; Exonuclease;
KW   Hydrolase; Magnesium; Metal-binding; Nuclease; Reference proteome.
FT   CHAIN           1..328
FT                   /note="Flap endonuclease 1"
FT                   /id="PRO_1000200238"
FT   REGION          1..100
FT                   /note="N-domain"
FT   REGION          120..248
FT                   /note="I-domain"
FT   REGION          320..328
FT                   /note="Interaction with PCNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         28
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         82
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         156
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         158
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         177
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         179
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT   BINDING         227
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
SQ   SEQUENCE   328 AA;  36413 MW;  CD0BC1844C1AB36B CRC64;
     MGNADLRTLA AIEPKPFDEL GGSVVAVDAH NWLYRYLTTT VKFTRSEAYT TADGEEVANL
     IGVVQGLPKF FEHDVTPVFV FDGGVSDLKA DEVEKRRDQR ERYEAQLEAA KERDETDAAE
     IAALESRTQR LTDTIVETTR ELLARLDVPV VEAPAEGEAQ AAHMARRGDA DYVGSEDYDA
     LLLGAPYTLR GLTSNGDPEC MDFEATLSTH DLSWEGLVDA AILMGTDFNE GLSGVGPKTA
     VKLIHEHGDL RSVLAARDDD IPHADRIREL FLDPAVTDDY DYDTDIDPDF ERAREFVTET
     WGVPADEVER GFERIEESVI QTGLDRWT
 
 
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