APE1L_ARATH
ID APE1L_ARATH Reviewed; 364 AA.
AC Q5XF07; Q9STM2;
DT 13-NOV-2013, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=DNA-(apurinic or apyrimidinic site) endonuclease {ECO:0000305};
DE EC=3.1.-.- {ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774};
DE AltName: Full=APEX1-like protein {ECO:0000303|PubMed:19172180};
DE AltName: Full=Apurinic-apyrimidinic endonuclease;
GN Name=APE1L {ECO:0000303|PubMed:19172180};
GN OrderedLocusNames=At3g48425 {ECO:0000312|Araport:AT3G48425};
GN ORFNames=T29H11.60 {ECO:0000312|EMBL:CAB41156.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19172180; DOI=10.1371/journal.pone.0004297;
RA Murphy T.M., Belmonte M., Shu S., Britt A.B., Hatteroth J.;
RT "Requirement for abasic endonuclease gene homologues in Arabidopsis seed
RT development.";
RL PLoS ONE 4:E4297-E4297(2009).
RN [5]
RP FUNCTION, TISSUE SPECIFICITY, CATALYTIC ACTIVITY, COFACTOR, AND
RP DNA-BINDING.
RX PubMed=25228464; DOI=10.1093/nar/gku834;
RA Lee J., Jang H., Shin H., Choi W.L., Mok Y.G., Huh J.H.;
RT "AP endonucleases process 5-methylcytosine excision intermediates during
RT active DNA demethylation in Arabidopsis.";
RL Nucleic Acids Res. 42:11408-11418(2014).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF ASN-224, INTERACTION
RP WITH ROS1, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=25569774; DOI=10.1371/journal.pgen.1004905;
RA Li Y., Cordoba-Canero D., Qian W., Zhu X., Tang K., Zhang H., Ariza R.R.,
RA Roldan-Arjona T., Zhu J.K.;
RT "An AP endonuclease functions in active DNA dimethylation and gene
RT imprinting in Arabidopsis.";
RL PLoS Genet. 11:E1004905-E1004905(2015).
CC -!- FUNCTION: Apurinic/apyrimidinic (AP) endonuclease involved in active
CC DNA demethylation and gene imprinting (PubMed:25569774). According to a
CC report, also displays an in vitro 3'-phosphatase activity
CC (PubMed:25569774). According to another report, has no in vitro 3'-
CC phosphatase activity (PubMed:25228464). Catalyzes the conversion of the
CC 3'-blocking groups 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA)
CC generated by ROS1 to 3'-OH (PubMed:25228464, PubMed:25569774). Has a
CC strong non-specific affinity to DNA (PubMed:25228464). Redundant with
CC APE2 and at least one functional allele is required for seed viability
CC (PubMed:19172180). {ECO:0000269|PubMed:19172180,
CC ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774};
CC Note=Probably binds two magnesium ions per subunit.
CC {ECO:0000250|UniProtKB:P27695};
CC -!- SUBUNIT: Interacts with ROS1 (PubMed:25569774). ROS1 is required for
CC APE1L to stably associate with the DNA substrate (PubMed:25569774).
CC {ECO:0000269|PubMed:25569774}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:25569774}. Nucleus,
CC nucleolus {ECO:0000269|PubMed:25569774}. Note=Co-localizes in
CC nucleoplasmic foci with ROS1 and ZDP, two components of the DNA
CC demethylase machinery. {ECO:0000269|PubMed:25569774}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, flower buds and developing
CC siliques. Not detected in roots. {ECO:0000269|PubMed:25228464}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:19172180,
CC PubMed:25569774). Ape1l ape2 double mutants are embryo lethal
CC (PubMed:19172180). Ape1l arp double mutants have no visible phenotype
CC (PubMed:19172180). Zdp ape1l double mutants are embryo lethal and cause
CC DNA hypermethylation and down-regulation of imprinted genes in the
CC endosperm (PubMed:25569774). {ECO:0000269|PubMed:19172180,
CC ECO:0000269|PubMed:25569774}.
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/exoA family.
CC {ECO:0000255|PROSITE-ProRule:PRU00764}.
CC -!- SEQUENCE CAUTION:
CC 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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DR EMBL; AL049659; CAB41156.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE78415.1; -; Genomic_DNA.
DR EMBL; BT015809; AAU94372.1; -; mRNA.
DR EMBL; BT020215; AAV59281.1; -; mRNA.
DR PIR; T06700; T06700.
DR RefSeq; NP_566904.2; NM_114702.3.
DR AlphaFoldDB; Q5XF07; -.
DR SMR; Q5XF07; -.
DR BioGRID; 9320; 1.
DR STRING; 3702.AT3G48425.1; -.
DR iPTMnet; Q5XF07; -.
DR PaxDb; Q5XF07; -.
DR PRIDE; Q5XF07; -.
DR ProteomicsDB; 240883; -.
DR EnsemblPlants; AT3G48425.1; AT3G48425.1; AT3G48425.
DR GeneID; 824001; -.
DR Gramene; AT3G48425.1; AT3G48425.1; AT3G48425.
DR KEGG; ath:AT3G48425; -.
DR Araport; AT3G48425; -.
DR TAIR; locus:505006392; AT3G48425.
DR eggNOG; KOG1294; Eukaryota.
DR HOGENOM; CLU_027539_6_0_1; -.
DR InParanoid; Q5XF07; -.
DR OMA; AFCQFVS; -.
DR OrthoDB; 1105625at2759; -.
DR PRO; PR:Q5XF07; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q5XF07; baseline and differential.
DR Genevisible; Q5XF07; AT.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0006284; P:base-excision repair; IBA:GO_Central.
DR Gene3D; 3.60.10.10; -; 1.
DR InterPro; IPR004808; AP_endonuc_1.
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; PS51435; AP_NUCLEASE_F1_4; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..364
FT /note="DNA-(apurinic or apyrimidinic site) endonuclease"
FT /id="PRO_0000424316"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 20..41
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 182
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT ACT_SITE 222
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT BINDING 80
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT BINDING 222
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT BINDING 224
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT BINDING 342
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT SITE 224
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT SITE 311
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT SITE 343
FT /note="Interaction with DNA substrate"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT MUTAGEN 224
FT /note="N->D: Loss of 3'-phosphatase activity and strongly
FT reduced AP endonuclease activity."
FT /evidence="ECO:0000269|PubMed:25569774"
SQ 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
