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FEN_PYRAB
ID   FEN_PYRAB               Reviewed;         343 AA.
AC   Q9V0P9; G8ZGU1;
DT   12-FEB-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   03-AUG-2022, entry version 118.
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=PYRAB07400;
GN   ORFNames=PAB1877;
OS   Pyrococcus abyssi (strain GE5 / Orsay).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=272844;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=GE5 / Orsay;
RX   PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA   Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA   Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA   Weissenbach J., Zivanovic Y., Forterre P.;
RT   "An integrated analysis of the genome of the hyperthermophilic archaeon
RT   Pyrococcus abyssi.";
RL   Mol. Microbiol. 47:1495-1512(2003).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=GE5 / Orsay;
RX   PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA   Gao J., Wang J.;
RT   "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT   Pyrococcus furiosus DSM 3638.";
RL   Curr. Microbiol. 64:118-129(2012).
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; AJ248285; CAB49654.1; -; Genomic_DNA.
DR   EMBL; HE613800; CCE70136.1; -; Genomic_DNA.
DR   PIR; E75117; E75117.
DR   RefSeq; WP_010867862.1; NC_000868.1.
DR   AlphaFoldDB; Q9V0P9; -.
DR   SMR; Q9V0P9; -.
DR   STRING; 272844.PAB1877; -.
DR   EnsemblBacteria; CAB49654; CAB49654; PAB1877.
DR   GeneID; 1495649; -.
DR   KEGG; pab:PAB1877; -.
DR   PATRIC; fig|272844.11.peg.780; -.
DR   eggNOG; arCOG04050; Archaea.
DR   HOGENOM; CLU_032444_0_0_2; -.
DR   OMA; GSQDYDS; -.
DR   OrthoDB; 41214at2157; -.
DR   PhylomeDB; Q9V0P9; -.
DR   BRENDA; 3.1.99.B1; 5242.
DR   Proteomes; UP000000810; Chromosome.
DR   Proteomes; UP000009139; 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.
FT   CHAIN           1..343
FT                   /note="Flap endonuclease 1"
FT                   /id="PRO_0000154059"
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"
SQ   SEQUENCE   343 AA;  38949 MW;  894A870642B545DD CRC64;
     MGVPIGELIP RKEIELENLY GKKIAIDALN AIYQFLSTIR QRDGTPLMDS KGRITSHLSG
     LFYRTINLME AGIKPVYVFD GKPPAFKKKE LEKRREAREE AEIKWKEALA KGDIEEARKY
     AQRATKVNEM LIEDAKKLLQ LMGIPIVQAP SEGEAQAAYM AGKGDVYASA SQDYDSLLFG
     TPRLVRNLTI TGKRKMPGKD IYVEIKPELI VLEEVLKELK ITREKLIELA ILVGTDYNPG
     GIKGIGPKKA LEIVKYSKDP LAKFQRQSDV DLYAIKEFFL NPPTTDDYSL KWKEPDEEGI
     IRFLCDEHDF SEERVKNGLE RLKKAIKAGK QSTLESWFIK KKP
 
 
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