FEN_ARCFU
ID FEN_ARCFU Reviewed; 336 AA.
AC O29975;
DT 12-FEB-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 133.
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=AF_0264;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH DNA AND PCNA.
RX PubMed=14718165; DOI=10.1016/s0092-8674(03)01036-5;
RA Chapados B.R., Hosfield D.J., Han S., Qiu J., Yelent B., Shen B.,
RA Tainer J.A.;
RT "Structural basis for FEN-1 substrate specificity and PCNA-mediated
RT activation in DNA replication and repair.";
RL Cell 116:39-50(2004).
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, ECO:0000269|PubMed:14718165}.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00614}.
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DR EMBL; AE000782; AAB90967.1; -; Genomic_DNA.
DR PIR; H69282; H69282.
DR RefSeq; WP_010877775.1; NC_000917.1.
DR PDB; 1RXV; X-ray; 2.50 A; A/B=1-336.
DR PDB; 1RXW; X-ray; 2.00 A; A=1-336.
DR PDB; 1RXZ; X-ray; 2.00 A; B=326-336.
DR PDBsum; 1RXV; -.
DR PDBsum; 1RXW; -.
DR PDBsum; 1RXZ; -.
DR AlphaFoldDB; O29975; -.
DR SMR; O29975; -.
DR STRING; 224325.AF_0264; -.
DR EnsemblBacteria; AAB90967; AAB90967; AF_0264.
DR GeneID; 24793800; -.
DR KEGG; afu:AF_0264; -.
DR eggNOG; arCOG04050; Archaea.
DR HOGENOM; CLU_032444_0_0_2; -.
DR OMA; GSQDYDS; -.
DR OrthoDB; 41214at2157; -.
DR PhylomeDB; O29975; -.
DR BRENDA; 3.1.99.B1; 414.
DR EvolutionaryTrace; O29975; -.
DR Proteomes; UP000002199; 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; IPR002421; 5-3_exonuclease.
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; SM00475; 53EXOc; 1.
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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA replication; Endonuclease;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome.
FT CHAIN 1..336
FT /note="Flap endonuclease 1"
FT /id="PRO_0000154050"
FT REGION 1..98
FT /note="N-domain"
FT REGION 115..256
FT /note="I-domain"
FT REGION 328..336
FT /note="Interaction with PCNA"
FT BINDING 27
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 80
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 151
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 172
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 235
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT HELIX 5..8
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 16..19
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 56..71
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 88..111
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 116..123
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 152..161
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 181..186
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 211..218
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 222..232
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 245..255
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 258..265
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 273..280
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 297..304
FT /evidence="ECO:0007829|PDB:1RXW"
FT TURN 305..308
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 312..319
FT /evidence="ECO:0007829|PDB:1RXW"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:1RXW"
FT STRAND 327..329
FT /evidence="ECO:0007829|PDB:1RXZ"
FT HELIX 332..334
FT /evidence="ECO:0007829|PDB:1RXZ"
SQ SEQUENCE 336 AA; 38065 MW; 68778F204FD96F00 CRC64;
MGADIGDLFE REEVELEYFS GKKIAVDAFN TLYQFISIIR QPDGTPLKDS QGRITSHLSG
ILYRVSNMVE VGIRPVFVFD GEPPEFKKAE IEERKKRRAE AEEMWIAALQ AGDKDAKKYA
QAAGRVDEYI VDSAKTLLSY MGIPFVDAPS EGEAQAAYMA AKGDVEYTGS QDYDSLLFGS
PRLARNLAIT GKRKLPGKNV YVDVKPEIII LESNLKRLGL TREQLIDIAI LVGTDYNEGV
KGVGVKKALN YIKTYGDIFR ALKALKVNID HVEEIRNFFL NPPVTDDYRI EFREPDFEKA
IEFLCEEHDF SRERVEKALE KLKALKSTQA TLERWF
