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DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX1-like protein) (Apurinic-apyrimidinic endonuclease)

 APE1L_ARATH             Reviewed;         364 AA.
Q5XF07; Q9STM2;
13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
23-NOV-2004, sequence version 1.
18-JUL-2018, entry version 92.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase {ECO:0000305};
EC=3.1.-.-;
EC=4.2.99.18 {ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774};
AltName: Full=APEX1-like protein {ECO:0000303|PubMed:19172180};
AltName: Full=Apurinic-apyrimidinic endonuclease;
Name=APE1L {ECO:0000303|PubMed:19172180};
OrderedLocusNames=At3g48425 {ECO:0000312|Araport:AT3G48425};
ORFNames=T29H11.60 {ECO:0000312|EMBL:CAB41156.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130713; DOI=10.1038/35048706;
Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M.,
Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B.,
Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P.,
De Simone V., Choisne N., Artiguenave F., Robert C., Brottier P.,
Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F.,
Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V.,
Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S.,
Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G.,
Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B.,
Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G.,
Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J.,
Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D.,
Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
Monfort A., Argiriou A., Flores M., Liguori R., Vitale D.,
Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W.,
Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J.,
Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P.,
Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S.,
Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V.,
Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C.,
Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E.,
Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y.,
Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A.,
Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
Watanabe A., Yamada M., Yasuda M., Tabata S.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
"Arabidopsis ORF clones.";
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
[4]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=19172180; DOI=10.1371/journal.pone.0004297;
Murphy T.M., Belmonte M., Shu S., Britt A.B., Hatteroth J.;
"Requirement for abasic endonuclease gene homologues in Arabidopsis
seed development.";
PLoS ONE 4:E4297-E4297(2009).
[5]
FUNCTION, TISSUE SPECIFICITY, CATALYTIC ACTIVITY, COFACTOR, AND
DNA-BINDING.
PubMed=25228464; DOI=10.1093/nar/gku834;
Lee J., Jang H., Shin H., Choi W.L., Mok Y.G., Huh J.H.;
"AP endonucleases process 5-methylcytosine excision intermediates
during active DNA demethylation in Arabidopsis.";
Nucleic Acids Res. 42:11408-11418(2014).
[6]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF ASN-224,
INTERACTION WITH ROS1, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=25569774; DOI=10.1371/journal.pgen.1004905;
Li Y., Cordoba-Canero D., Qian W., Zhu X., Tang K., Zhang H.,
Ariza R.R., Roldan-Arjona T., Zhu J.K.;
"An AP endonuclease functions in active DNA dimethylation and gene
imprinting in Arabidopsis.";
PLoS Genet. 11:E1004905-E1004905(2015).
-!- FUNCTION: Apurinic/apyrimidinic (AP) endonuclease involved in
active DNA demethylation and gene imprinting (PubMed:25569774).
According to a report, displays also an in vitro 3'-phosphatase
activity (PubMed:25569774). According to another report, has no in
vitro 3'-phosphatase activity (PubMed:25228464). Catalyzes the
conversion of the 3'-blocking groups 3'-phosphor-alpha,beta-
unsaturated aldehyde (3'-PUA) generated by ROS1 to 3'-OH
(PubMed:25228464, PubMed:25569774). Has a strong non-specific
affinity to DNA (PubMed:25228464). Redundant with APE2 and at
least one functional allele is required for seed viability
(PubMed:19172180). {ECO:0000269|PubMed:19172180,
ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774}.
-!- 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:0000269|PubMed:25228464,
ECO:0000269|PubMed:25569774}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:25228464,
ECO:0000269|PubMed:25569774};
Note=Probably binds two magnesium ions per subunit.
{ECO:0000250|UniProtKB:P27695};
-!- SUBUNIT: Interacts with ROS1 (PubMed:25569774). ROS1 is required
for APE1L to stably associate with the DNA substrate
(PubMed:25569774). {ECO:0000269|PubMed:25569774}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25569774}.
Nucleus, nucleolus {ECO:0000269|PubMed:25569774}. Note=Co-
localizes in nucleoplasmic foci with ROS1 and ZDP, two components
of the DNA demethylase machinery. {ECO:0000269|PubMed:25569774}.
-!- TISSUE SPECIFICITY: Expressed in leaves, flower buds and
developing siliques. Not detected in roots.
{ECO:0000269|PubMed:25228464}.
-!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:19172180,
PubMed:25569774). Ape1l ape2 double mutants are embryo lethal
(PubMed:19172180). Ape1l arp double mutants have no visible
phenotype (PubMed:19172180). Zdp ape1l double mutants are embryo
lethal and cause DNA hypermethylation and down-regulation of
imprinted genes in the endosperm (PubMed:25569774).
{ECO:0000269|PubMed:19172180, ECO:0000269|PubMed:25569774}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/exoA family.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
-!- SEQUENCE CAUTION:
Sequence=CAB41156.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At3g48420 and At3g48425.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AL049659; CAB41156.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002686; AEE78415.1; -; Genomic_DNA.
EMBL; BT015809; AAU94372.1; -; mRNA.
EMBL; BT020215; AAV59281.1; -; mRNA.
PIR; T06700; T06700.
RefSeq; NP_566904.2; NM_114702.3.
UniGene; At.50257; -.
ProteinModelPortal; Q5XF07; -.
SMR; Q5XF07; -.
BioGrid; 9320; 1.
STRING; 3702.AT3G48425.1; -.
iPTMnet; Q5XF07; -.
PaxDb; Q5XF07; -.
PRIDE; Q5XF07; -.
EnsemblPlants; AT3G48425.1; AT3G48425.1; AT3G48425.
GeneID; 824001; -.
Gramene; AT3G48425.1; AT3G48425.1; AT3G48425.
KEGG; ath:AT3G48425; -.
Araport; AT3G48425; -.
TAIR; locus:505006392; AT3G48425.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
InParanoid; Q5XF07; -.
OMA; FSWSGHP; -.
OrthoDB; EOG09360ET4; -.
Reactome; R-ATH-110357; Displacement of DNA glycosylase by APEX1.
Reactome; R-ATH-110373; Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
Reactome; R-ATH-5651801; PCNA-Dependent Long Patch Base Excision Repair.
Reactome; R-ATH-73933; Resolution of Abasic Sites (AP sites).
PRO; PR:Q5XF07; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q5XF07; baseline and differential.
Genevisible; Q5XF07; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
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: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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
Gene3D; 3.60.10.10; -; 1.
InterPro; IPR004808; AP_endonuc_1.
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; PS51435; AP_NUCLEASE_F1_4; 1.
1: Evidence at protein level;
Complete proteome; DNA damage; DNA repair; Hydrolase; Lyase;
Magnesium; Metal-binding; Nucleus; Reference proteome.
CHAIN 1 364 DNA-(apurinic or apyrimidinic site)
lyase.
/FTId=PRO_0000424316.
ACT_SITE 182 182 {ECO:0000250|UniProtKB:P27695}.
ACT_SITE 222 222 Proton donor/acceptor.
{ECO:0000250|UniProtKB:P27695}.
METAL 80 80 Magnesium 1.
{ECO:0000250|UniProtKB:P27695}.
METAL 222 222 Magnesium 2.
{ECO:0000250|UniProtKB:P27695}.
METAL 224 224 Magnesium 2.
{ECO:0000250|UniProtKB:P27695}.
METAL 342 342 Magnesium 1.
{ECO:0000250|UniProtKB:P27695}.
SITE 224 224 Transition state stabilizer.
{ECO:0000250|UniProtKB:P27695}.
SITE 311 311 Important for catalytic activity.
{ECO:0000250|UniProtKB:P27695}.
SITE 343 343 Interaction with DNA substrate.
{ECO:0000250|UniProtKB:P27695}.
MUTAGEN 224 224 N->D: Loss of 3'-phosphatase activity and
strongly reduced AP endonuclease
activity. {ECO:0000269|PubMed:25569774}.
SEQUENCE 364 AA; 41783 MW; E45B538512B8DCB3 CRC64;
MKRFFKPIEK ENSPAAKKPC LSPEKRDGDG DGVEEEKNQN EPSKFMTWNA NSFLLRVKND
WSQFSKFVSD FDPDVIAIQE VRMPAAGGKG KPKNHEELSD DTKVLREEKQ ILTRALSSPP
FGNYGVWWSL ADSKYAGTAL LVKKCFKPRK VYFNLDKLAS KHEPDGRVIL AEFETFRLLN
TYSPNNGWKD EENAFQRRRK WDKRIVEFLN KTSDKPLIWC GDLNVSHEEI DVSHPEFFAT
AKLNGYVPPN KEDCGQPGFT PSERGRFGAT IKEGRLVDAY RYLHKEQEME SGFSWSGNPI
GKYRGKRMRI DYFLVSEQLK DRIVSCKMHG RGIELEGFHG SDHCPVTLEL SKPSSEMEQN
QVSN


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