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DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (zAP1)

 APEX1_DANRE             Reviewed;         310 AA.
A0MTA1; Q4V955; Q5RHZ7; Q7SXL6;
11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
12-DEC-2006, sequence version 1.
23-MAY-2018, entry version 76.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase;
EC=3.1.-.-;
EC=4.2.99.18;
AltName: Full=APEX nuclease;
Short=APEN;
AltName: Full=Apurinic-apyrimidinic endonuclease 1;
Short=AP endonuclease 1;
Short=zAP1;
Name=apex1; Synonyms=apex1a, apex1b;
ORFNames=si:ch211-214j24.12, zgc:66204;
Danio rerio (Zebrafish) (Brachydanio rerio).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
Cyprinidae; Danio.
NCBI_TaxID=7955;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, AND DEVELOPMENTAL
STAGE.
TISSUE=Embryo;
PubMed=16966376; DOI=10.1128/MCB.01216-06;
Wang Y., Shupenko C.C., Melo L.F., Strauss P.R.;
"DNA repair protein involved in heart and blood development.";
Mol. Cell. Biol. 26:9083-9093(2006).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Tuebingen;
PubMed=23594743; DOI=10.1038/nature12111;
Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C.,
Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L.,
McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C.,
Koch R., Rauch G.J., White S., Chow W., Kilian B., Quintais L.T.,
Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T.,
Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F.,
Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H.,
Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G.,
Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B.,
Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S.,
Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C.,
Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H.,
Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C.,
Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
Humphries M., Sycamore N., Barker D., Saunders D., Wallis J.,
Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S.,
Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R.,
Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R.,
Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R.,
Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A.,
Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S.,
Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J.,
Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C.,
Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H.,
Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J.,
Stemple D.L.;
"The zebrafish reference genome sequence and its relationship to the
human genome.";
Nature 496:498-503(2013).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Olfactory epithelium;
NIH - Zebrafish Gene Collection (ZGC) project;
Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
[4]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 33-310, FUNCTION, AND
MUTAGENESIS OF THR-58.
PubMed=18579163; DOI=10.1016/j.mrfmmm.2008.04.008;
Georgiadis M.M., Luo M., Gaur R.K., Delaplane S., Li X., Kelley M.R.;
"Evolution of the redox function in mammalian apurinic/apyrimidinic
endonuclease.";
Mutat. Res. 643:54-63(2008).
-!- FUNCTION: Function as a apurinic/apyrimidinic (AP)
endodeoxyribonuclease in the DNA base excision repair (BER)
pathway of DNA lesions induced by oxidative and alkylating agents.
Initiates repair of AP sites in DNA by catalyzing hydrolytic
incision of the phosphodiester backbone immediately adjacent to
the damage, generating a single-strand break with 5'-deoxyribose
phosphate and 3'-hydroxyl ends. May also play a role in the
epigenetic regulation of gene expression by participating in DNA
demethylation. Required for passage through the midblastula
transition MBT. May also act as an endoribonuclease involved in
the control of single-stranded RNA metabolism. Has no redox
activity. Binds DNA and RNA. {ECO:0000269|PubMed:16966376,
ECO:0000269|PubMed:18579163}.
-!- CATALYTIC ACTIVITY: The C-O-P bond 3' to the apurinic or
apyrimidinic site in DNA is broken by a beta-elimination reaction,
leaving a 3'-terminal unsaturated sugar and a product with a
terminal 5'-phosphate. {ECO:0000255|PROSITE-ProRule:PRU00764}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Probably binds two magnesium or manganese ions per subunit.
{ECO:0000250};
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00764}. Nucleus, nucleolus {ECO:0000250}. Nucleus
speckle {ECO:0000255|PROSITE-ProRule:PRU00764}. Endoplasmic
reticulum {ECO:0000250}. Cytoplasm {ECO:0000255|PROSITE-
ProRule:PRU00764}. Mitochondrion {ECO:0000250}.
-!- DEVELOPMENTAL STAGE: Expressed in unfertilized eggs and embryos at
two stages (at protein level). Expressed throughout embryogenesis.
{ECO:0000269|PubMed:16966376}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; EF041101; ABK35081.1; -; mRNA.
EMBL; EF041102; ABK35082.1; -; mRNA.
EMBL; EF041103; ABK35083.1; -; Genomic_DNA.
EMBL; EF041104; ABK35084.1; -; Genomic_DNA.
EMBL; BX323558; CAI11781.1; -; Genomic_DNA.
EMBL; BC055545; AAH55545.1; -; mRNA.
EMBL; BC097053; AAH97053.1; -; mRNA.
EMBL; BC164240; AAI64240.1; -; mRNA.
UniGene; Dr.20170; -.
PDB; 2O3C; X-ray; 2.30 A; A/B/C=33-310.
PDBsum; 2O3C; -.
ProteinModelPortal; A0MTA1; -.
SMR; A0MTA1; -.
STRING; 7955.ENSDARP00000067373; -.
PaxDb; A0MTA1; -.
PeptideAtlas; A0MTA1; -.
PRIDE; A0MTA1; -.
ZFIN; ZDB-GENE-040426-2761; apex1.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
HOGENOM; HOG000034586; -.
HOVERGEN; HBG050531; -.
InParanoid; A0MTA1; -.
PhylomeDB; A0MTA1; -.
TreeFam; TF315048; -.
EvolutionaryTrace; A0MTA1; -.
PRO; PR:A0MTA1; -.
Proteomes; UP000000437; Unplaced.
GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IBA:GO_Central.
GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
GO; GO:0080111; P:DNA demethylation; ISS:UniProtKB.
GO; GO:0060047; P:heart contraction; IMP:ZFIN.
GO; GO:0001947; P:heart looping; IMP:ZFIN.
GO; GO:0043066; P:negative regulation of apoptotic process; IMP:ZFIN.
GO; GO:0010628; P:positive regulation of gene expression; IMP:ZFIN.
Gene3D; 3.60.10.10; -; 1.
InterPro; IPR004808; AP_endonuc_1.
InterPro; IPR020847; AP_endonuclease_F1_BS.
InterPro; IPR020848; AP_endonuclease_F1_CS.
InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
InterPro; IPR005135; Endo/exonuclease/phosphatase.
PANTHER; PTHR22748; PTHR22748; 1.
Pfam; PF03372; Exo_endo_phos; 1.
SUPFAM; SSF56219; SSF56219; 1.
TIGRFAMs; TIGR00633; xth; 1.
PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; DNA damage; DNA repair;
DNA-binding; Endonuclease; Endoplasmic reticulum; Hydrolase; Lyase;
Magnesium; Metal-binding; Mitochondrion; Nuclease; Nucleus;
Reference proteome; RNA-binding.
CHAIN 1 310 DNA-(apurinic or apyrimidinic site)
lyase.
/FTId=PRO_0000402575.
ACT_SITE 164 164 {ECO:0000250}.
ACT_SITE 203 203 Proton donor/acceptor. {ECO:0000250}.
METAL 63 63 Magnesium 1. {ECO:0000250}.
METAL 89 89 Magnesium 1. {ECO:0000250}.
METAL 203 203 Magnesium 2. {ECO:0000250}.
METAL 205 205 Magnesium 2. {ECO:0000250}.
METAL 300 300 Magnesium 1. {ECO:0000250}.
SITE 205 205 Transition state stabilizer.
{ECO:0000250}.
SITE 275 275 Important for catalytic activity.
{ECO:0000250}.
SITE 301 301 Interaction with DNA substrate.
{ECO:0000250}.
MUTAGEN 58 58 T->C: Confers redox activity.
{ECO:0000269|PubMed:18579163}.
CONFLICT 16 16 A -> S (in Ref. 2; CAI11781).
{ECO:0000305}.
CONFLICT 80 93 Missing (in Ref. 3; AAI64240/AAH97053).
{ECO:0000305}.
CONFLICT 103 103 G -> A (in Ref. 3; AAH55545).
{ECO:0000305}.
STRAND 55 61 {ECO:0000244|PDB:2O3C}.
HELIX 65 70 {ECO:0000244|PDB:2O3C}.
HELIX 73 80 {ECO:0000244|PDB:2O3C}.
STRAND 83 88 {ECO:0000244|PDB:2O3C}.
HELIX 94 96 {ECO:0000244|PDB:2O3C}.
HELIX 99 102 {ECO:0000244|PDB:2O3C}.
STRAND 108 113 {ECO:0000244|PDB:2O3C}.
STRAND 124 130 {ECO:0000244|PDB:2O3C}.
STRAND 133 138 {ECO:0000244|PDB:2O3C}.
TURN 142 146 {ECO:0000244|PDB:2O3C}.
STRAND 150 154 {ECO:0000244|PDB:2O3C}.
STRAND 159 164 {ECO:0000244|PDB:2O3C}.
HELIX 170 172 {ECO:0000244|PDB:2O3C}.
HELIX 175 195 {ECO:0000244|PDB:2O3C}.
STRAND 198 203 {ECO:0000244|PDB:2O3C}.
HELIX 210 212 {ECO:0000244|PDB:2O3C}.
HELIX 216 219 {ECO:0000244|PDB:2O3C}.
HELIX 227 238 {ECO:0000244|PDB:2O3C}.
STRAND 241 243 {ECO:0000244|PDB:2O3C}.
HELIX 244 248 {ECO:0000244|PDB:2O3C}.
HELIX 262 264 {ECO:0000244|PDB:2O3C}.
HELIX 265 268 {ECO:0000244|PDB:2O3C}.
STRAND 275 280 {ECO:0000244|PDB:2O3C}.
HELIX 281 286 {ECO:0000244|PDB:2O3C}.
STRAND 287 292 {ECO:0000244|PDB:2O3C}.
STRAND 298 301 {ECO:0000244|PDB:2O3C}.
STRAND 304 308 {ECO:0000244|PDB:2O3C}.
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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