FEN_METJA
ID FEN_METJA Reviewed; 326 AA.
AC Q58839;
DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 135.
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=MJ1444;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP CHARACTERIZATION.
RX PubMed=9765572; DOI=10.1128/jb.180.20.5406-5412.1998;
RA Rao H.G., Rosenfeld A., Wetmur J.G.;
RT "Methanococcus jannaschii flap endonuclease: expression, purification, and
RT substrate requirements.";
RL J. Bacteriol. 180:5406-5412(1998).
RN [3]
RP CHARACTERIZATION, AND X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
RX PubMed=10102570;
RA Bae K.W., Baek K.W., Cho C.S., Hwang K.Y., Kim H.-R., Sung H.-C., Cho Y.;
RT "Expression, purification, characterization and crystallization of flap
RT endonuclease-1 from Methanococcus jannaschii.";
RL Mol. Cells 9:45-48(1999).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=9699635; DOI=10.1038/1406;
RA Hwang K.Y., Baek K., Kim H.-Y., Cho Y.;
RT "The crystal structure of flap endonuclease-1 from Methanococcus
RT jannaschii.";
RL Nat. Struct. Biol. 5:707-713(1998).
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.
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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6-7.;
CC -!- SUBUNIT: Interacts with PCNA. PCNA stimulates the nuclease activity
CC without altering cleavage specificity.
CC -!- SIMILARITY: Belongs to the XPG/RAD2 endonuclease family. FEN1
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00614}.
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DR EMBL; L77117; AAB99454.1; -; Genomic_DNA.
DR PIR; C64480; C64480.
DR RefSeq; WP_010870964.1; NC_000909.1.
DR PDB; 1A76; X-ray; 2.00 A; A=1-326.
DR PDB; 1A77; X-ray; 2.00 A; A=1-326.
DR PDBsum; 1A76; -.
DR PDBsum; 1A77; -.
DR AlphaFoldDB; Q58839; -.
DR SMR; Q58839; -.
DR STRING; 243232.MJ_1444; -.
DR EnsemblBacteria; AAB99454; AAB99454; MJ_1444.
DR GeneID; 1452348; -.
DR KEGG; mja:MJ_1444; -.
DR eggNOG; arCOG04050; Archaea.
DR HOGENOM; CLU_032444_0_0_2; -.
DR InParanoid; Q58839; -.
DR OMA; GSQDYDS; -.
DR OrthoDB; 41214at2157; -.
DR PhylomeDB; Q58839; -.
DR BRENDA; 3.1.99.B1; 3260.
DR EvolutionaryTrace; Q58839; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0008409; F:5'-3' exonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0017108; F:5'-flap endonuclease activity; IBA:GO_Central.
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; 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.
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..326
FT /note="Flap endonuclease 1"
FT /id="PRO_0000154053"
FT REGION 1..98
FT /note="N-domain"
FT REGION 116..245
FT /note="I-domain"
FT REGION 317..325
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:0000269|PubMed:9699635,
FT ECO:0007744|PDB:1A77"
FT BINDING 154
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:9699635,
FT ECO:0007744|PDB:1A76, ECO:0007744|PDB:1A77"
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 224
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:9699635,
FT ECO:0007744|PDB:1A76, ECO:0007744|PDB:1A77"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 23..27
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 56..70
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 111..115
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 121..124
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 129..142
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 153..162
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 175..179
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 182..190
FT /evidence="ECO:0007829|PDB:1A76"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 200..207
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 211..221
FT /evidence="ECO:0007829|PDB:1A76"
FT TURN 227..232
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 235..243
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 247..254
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 258..266
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 283..290
FT /evidence="ECO:0007829|PDB:1A76"
FT TURN 291..294
FT /evidence="ECO:0007829|PDB:1A76"
FT HELIX 298..315
FT /evidence="ECO:0007829|PDB:1A76"
SQ SEQUENCE 326 AA; 37527 MW; 311427F2B4B67580 CRC64;
MGVQFGDFIP KNIISFEDLK GKKVAIDGMN ALYQFLTSIR LRDGSPLRNR KGEITSAYNG
VFYKTIHLLE NDITPIWVFD GEPPKLKEKT RKVRREMKEK AELKMKEAIK KEDFEEAAKY
AKRVSYLTPK MVENCKYLLS LMGIPYVEAP SEGEAQASYM AKKGDVWAVV SQDYDALLYG
APRVVRNLTT TKEMPELIEL NEVLEDLRIS LDDLIDIAIF MGTDYNPGGV KGIGFKRAYE
LVRSGVAKDV LKKEVEYYDE IKRIFKEPKV TDNYSLSLKL PDKEGIIKFL VDENDFNYDR
VKKHVDKLYN LIANKTKQKT LDAWFK
