FEN_PYRHO
ID FEN_PYRHO Reviewed; 343 AA.
AC O50123;
DT 12-FEB-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 130.
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=PH1415;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
RX PubMed=12147694; DOI=10.1074/jbc.m205235200;
RA Matsui E., Musti K.V., Abe J., Yamasaki K., Matsui I., Harata K.;
RT "Molecular structure and novel DNA binding sites located in loops of flap
RT endonuclease-1 from Pyrococcus horikoshii.";
RL J. Biol. Chem. 277:37840-37847(2002).
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; BA000001; BAA30521.1; -; Genomic_DNA.
DR PIR; A71015; A71015.
DR RefSeq; WP_010885498.1; NC_000961.1.
DR PDB; 1MC8; X-ray; 3.10 A; A/B=1-343.
DR PDBsum; 1MC8; -.
DR AlphaFoldDB; O50123; -.
DR SMR; O50123; -.
DR STRING; 70601.3257838; -.
DR EnsemblBacteria; BAA30521; BAA30521; BAA30521.
DR GeneID; 1443736; -.
DR KEGG; pho:PH1415; -.
DR eggNOG; arCOG04050; Archaea.
DR OMA; GSQDYDS; -.
DR OrthoDB; 41214at2157; -.
DR BRENDA; 3.1.99.B1; 5244.
DR EvolutionaryTrace; O50123; -.
DR Proteomes; UP000000752; 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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA replication; Endonuclease;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease.
FT CHAIN 1..343
FT /note="Flap endonuclease 1"
FT /id="PRO_0000154062"
FT REGION 1..98
FT /note="N-domain"
FT REGION 116..258
FT /note="I-domain"
FT REGION 330..338
FT /note="Interaction with PCNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
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 152
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 154
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 173
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 175
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00614"
FT BINDING 236
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:1MC8"
FT TURN 16..21
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 56..71
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 102..107
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 117..124
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 129..142
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 153..161
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 175..178
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 182..186
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 208..211
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 212..217
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 223..233
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 247..255
FT /evidence="ECO:0007829|PDB:1MC8"
FT STRAND 256..259
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 265..268
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 273..280
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 297..304
FT /evidence="ECO:0007829|PDB:1MC8"
FT TURN 305..308
FT /evidence="ECO:0007829|PDB:1MC8"
FT HELIX 312..327
FT /evidence="ECO:0007829|PDB:1MC8"
SQ SEQUENCE 343 AA; 38947 MW; 8BE0025F372C3138 CRC64;
MGVPIGDLVP RKEIDLENLY GKKIAIDALN AIYQFLSTIR QRDGTPLMDS KGRITSHLSG
LFYRTINLME AGIKPAYVFD GKPPEFKRKE LEKRREAREE AELKWKEALA KGNLEEARKY
AQRATKVNEM LIEDAKKLLQ LMGIPIIQAP SEGEAQAAYM ASKGDVYASA SQDYDSLLFG
APRLIRNLTI TGKRKMPGKD VYVEIKPELV VLDEVLKELK ITREKLIELA ILVGTDYNPG
GVKGIGPKKA LEIVRYSRDP LAKFQRQSDV DLYAIKEFFL NPPVTNEYSL SWKEPDEEGI
LKFLCDEHNF SEERVKNGIE RLKKAIKAGR QSTLESWFVK KKP
