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APEX1_DANRE
ID   APEX1_DANRE             Reviewed;         310 AA.
AC   A0MTA1; Q4V955; Q5RHZ7; Q7SXL6;
DT   11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT   12-DEC-2006, sequence version 1.
DT   03-AUG-2022, entry version 92.
DE   RecName: Full=DNA-(apurinic or apyrimidinic site) endonuclease;
DE            EC=3.1.11.2 {ECO:0000250|UniProtKB:P27695};
DE   AltName: Full=APEX nuclease;
DE            Short=APEN;
DE   AltName: Full=Apurinic-apyrimidinic endonuclease 1;
DE            Short=AP endonuclease 1;
DE            Short=zAP1;
GN   Name=apex1; Synonyms=apex1a, apex1b;
GN   ORFNames=si:ch211-214j24.12, zgc:66204;
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, AND DEVELOPMENTAL
RP   STAGE.
RC   TISSUE=Embryo;
RX   PubMed=16966376; DOI=10.1128/mcb.01216-06;
RA   Wang Y., Shupenko C.C., Melo L.F., Strauss P.R.;
RT   "DNA repair protein involved in heart and blood development.";
RL   Mol. Cell. Biol. 26:9083-9093(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
RX   PubMed=23594743; DOI=10.1038/nature12111;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA   Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA   Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA   Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA   Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA   Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA   Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA   McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA   Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA   Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA   Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA   Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA   Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA   Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA   Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA   Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA   Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA   Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA   Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA   Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA   de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA   Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Olfactory epithelium;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 33-310, FUNCTION, AND MUTAGENESIS
RP   OF THR-58.
RX   PubMed=18579163; DOI=10.1016/j.mrfmmm.2008.04.008;
RA   Georgiadis M.M., Luo M., Gaur R.K., Delaplane S., Li X., Kelley M.R.;
RT   "Evolution of the redox function in mammalian apurinic/apyrimidinic
RT   endonuclease.";
RL   Mutat. Res. 643:54-63(2008).
CC   -!- FUNCTION: Functions as a apurinic/apyrimidinic (AP)
CC       endodeoxyribonuclease in the DNA base excision repair (BER) pathway of
CC       DNA lesions induced by oxidative and alkylating agents. Initiates
CC       repair of AP sites in DNA by catalyzing hydrolytic incision of the
CC       phosphodiester backbone immediately adjacent to the damage, generating
CC       a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl
CC       ends. May also play a role in the epigenetic regulation of gene
CC       expression by participating in DNA demethylation. Required for passage
CC       through the midblastula transition MBT. May also act as an
CC       endoribonuclease involved in the control of single-stranded RNA
CC       metabolism. Has no redox activity. Binds DNA and RNA.
CC       {ECO:0000269|PubMed:16966376, ECO:0000269|PubMed:18579163}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC         nucleoside 5'-phosphates.; EC=3.1.11.2;
CC         Evidence={ECO:0000250|UniProtKB:P27695};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Probably binds two magnesium or manganese ions per subunit.
CC       {ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00764}.
CC       Nucleus, nucleolus {ECO:0000250}. Nucleus speckle {ECO:0000255|PROSITE-
CC       ProRule:PRU00764}. Endoplasmic reticulum {ECO:0000250}. Cytoplasm
CC       {ECO:0000255|PROSITE-ProRule:PRU00764}. Mitochondrion {ECO:0000250}.
CC   -!- DEVELOPMENTAL STAGE: Expressed in unfertilized eggs and embryos at two
CC       stages (at protein level). Expressed throughout embryogenesis.
CC       {ECO:0000269|PubMed:16966376}.
CC   -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC       {ECO:0000305}.
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DR   EMBL; EF041101; ABK35081.1; -; mRNA.
DR   EMBL; EF041102; ABK35082.1; -; mRNA.
DR   EMBL; EF041103; ABK35083.1; -; Genomic_DNA.
DR   EMBL; EF041104; ABK35084.1; -; Genomic_DNA.
DR   EMBL; BX323558; CAI11781.1; -; Genomic_DNA.
DR   EMBL; BC055545; AAH55545.1; -; mRNA.
DR   EMBL; BC097053; AAH97053.1; -; mRNA.
DR   EMBL; BC164240; AAI64240.1; -; mRNA.
DR   PDB; 2O3C; X-ray; 2.30 A; A/B/C=33-310.
DR   PDBsum; 2O3C; -.
DR   AlphaFoldDB; A0MTA1; -.
DR   SMR; A0MTA1; -.
DR   STRING; 7955.ENSDARP00000067373; -.
DR   PaxDb; A0MTA1; -.
DR   PeptideAtlas; A0MTA1; -.
DR   PRIDE; A0MTA1; -.
DR   ZFIN; ZDB-GENE-040426-2761; apex1.
DR   eggNOG; KOG1294; Eukaryota.
DR   InParanoid; A0MTA1; -.
DR   PhylomeDB; A0MTA1; -.
DR   TreeFam; TF315048; -.
DR   Reactome; R-DRE-110357; Displacement of DNA glycosylase by APEX1.
DR   Reactome; R-DRE-110362; POLB-Dependent Long Patch Base Excision Repair.
DR   Reactome; R-DRE-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
DR   Reactome; R-DRE-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR   Reactome; R-DRE-73930; Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
DR   Reactome; R-DRE-73933; Resolution of Abasic Sites (AP sites).
DR   EvolutionaryTrace; A0MTA1; -.
DR   PRO; PR:A0MTA1; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Unplaced.
DR   GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR   GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0052720; F:class II DNA-(apurinic or apyrimidinic site) endonuclease activity; ISS:UniProtKB.
DR   GO; GO:0140431; F:DNA-(abasic site) binding; ISS:UniProtKB.
DR   GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IBA:GO_Central.
DR   GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008081; F:phosphoric diester hydrolase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
DR   GO; GO:0080111; P:DNA demethylation; ISS:UniProtKB.
DR   GO; GO:0060047; P:heart contraction; IMP:ZFIN.
DR   GO; GO:0001947; P:heart looping; IMP:ZFIN.
DR   GO; GO:0043066; P:negative regulation of apoptotic process; IMP:ZFIN.
DR   GO; GO:0010628; P:positive regulation of gene expression; IMP:ZFIN.
DR   Gene3D; 3.60.10.10; -; 1.
DR   InterPro; IPR004808; AP_endonuc_1.
DR   InterPro; IPR020847; AP_endonuclease_F1_BS.
DR   InterPro; IPR020848; AP_endonuclease_F1_CS.
DR   InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR   InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR   PANTHER; PTHR22748; PTHR22748; 1.
DR   Pfam; PF03372; Exo_endo_phos; 1.
DR   SUPFAM; SSF56219; SSF56219; 1.
DR   TIGRFAMs; TIGR00633; xth; 1.
DR   PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR   PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
DR   PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; DNA damage; DNA repair; DNA-binding; Endonuclease;
KW   Endoplasmic reticulum; Hydrolase; Magnesium; Metal-binding; Mitochondrion;
KW   Nuclease; Nucleus; Reference proteome; RNA-binding.
FT   CHAIN           1..310
FT                   /note="DNA-(apurinic or apyrimidinic site) endonuclease"
FT                   /id="PRO_0000402575"
FT   REGION          1..51
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..50
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        164
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        203
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         63
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         89
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         203
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         205
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         300
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   SITE            205
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250"
FT   SITE            275
FT                   /note="Important for catalytic activity"
FT                   /evidence="ECO:0000250"
FT   SITE            301
FT                   /note="Interaction with DNA substrate"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         58
FT                   /note="T->C: Confers redox activity."
FT                   /evidence="ECO:0000269|PubMed:18579163"
FT   CONFLICT        16
FT                   /note="A -> S (in Ref. 2; CAI11781)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        80..93
FT                   /note="Missing (in Ref. 3; AAI64240/AAH97053)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        103
FT                   /note="G -> A (in Ref. 3; AAH55545)"
FT                   /evidence="ECO:0000305"
FT   STRAND          55..61
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           65..70
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           73..80
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          83..88
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           94..96
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           99..102
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          108..113
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          124..130
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          133..138
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   TURN            142..146
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          150..154
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          159..164
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           170..172
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           175..195
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          198..203
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           210..212
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           216..219
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           227..238
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          241..243
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           244..248
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           262..264
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           265..268
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          275..280
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   HELIX           281..286
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          287..292
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          298..301
FT                   /evidence="ECO:0007829|PDB:2O3C"
FT   STRAND          304..308
FT                   /evidence="ECO:0007829|PDB:2O3C"
SQ   SEQUENCE   310 AA;  34881 MW;  F57493D443106F4B CRC64;
     MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG RAANMKITSW
     NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD ITGMPEYPHK YWAGSEDKEG
     YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV ITAEFPDFFL VTAYVPNASR GLVRLDYRKT
     WDVDFRAYLC GLDARKPLVL CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG
     FTDSFRELYP DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD
     HCPITLFLAV
 
 
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