APE2_ARATH
ID APE2_ARATH Reviewed; 610 AA.
AC F4JNY0; C0Z270; O65642; Q8W4I0;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 75.
DE RecName: Full=DNA-(apurinic or apyrimidinic site) endonuclease 2 {ECO:0000303|PubMed:19172180};
DE EC=3.1.-.- {ECO:0000269|PubMed:25569774};
DE AltName: Full=Apurinic-apyrimidinic endonuclease 2;
GN Name=APE2 {ECO:0000303|PubMed:19172180};
GN OrderedLocusNames=At4g36050 {ECO:0000312|Araport:AT4G36050};
GN ORFNames=T19K4.180 {ECO:0000312|EMBL:CAA18499.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf {ECO:0000312|EMBL:BAH56799.1};
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
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 [6]
RP FUNCTION, TISSUE SPECIFICITY, LACK OF 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 [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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: Exhibits apurinic/apyrimidinic (AP) endonuclease activity in
CC vitro (PubMed:25569774). By contrast, another report show that APE2 has
CC no biochemical activity (PubMed:25228464). Unable to catalyze the
CC conversion of 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) to
CC 3'-OH (PubMed:25228464, PubMed:25569774). Has no in vitro 3'-
CC phosphatase activity (PubMed:25228464, PubMed:25569774). Redundant with
CC APE1L and at least one functional allele is required for seed viability
CC (PubMed:19172180). Has a strong non-specific affinity to DNA
CC (PubMed:25228464). {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};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P27695};
CC Note=Probably binds two magnesium or manganese ions per subunit.
CC {ECO:0000250|UniProtKB:P27695};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00764}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=F4JNY0-1; Sequence=Displayed;
CC Name=2;
CC IsoId=F4JNY0-2; Sequence=VSP_057574, VSP_057575;
CC Name=3;
CC IsoId=F4JNY0-3; Sequence=VSP_057574;
CC -!- TISSUE SPECIFICITY: Expressed in both vegetative and reproductive
CC organs. {ECO:0000269|PubMed:25228464}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:19172180). Ape2 arp
CC double mutants have no visible phenotype (PubMed:19172180). Ape1l ape2
CC double mutants are embryo lethal (PubMed:19172180).
CC {ECO:0000269|PubMed:19172180}.
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/exoA family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA18499.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB81514.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL022373; CAA18499.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161588; CAB81514.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE86606.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86607.1; -; Genomic_DNA.
DR EMBL; AY062550; AAL32628.1; -; mRNA.
DR EMBL; AY093329; AAM13328.1; -; mRNA.
DR EMBL; AK318684; BAH56799.1; -; mRNA.
DR PIR; T05497; T05497.
DR RefSeq; NP_195329.2; NM_119772.3. [F4JNY0-2]
DR RefSeq; NP_974691.2; NM_202962.2. [F4JNY0-1]
DR AlphaFoldDB; F4JNY0; -.
DR SMR; F4JNY0; -.
DR STRING; 3702.AT4G36050.2; -.
DR iPTMnet; F4JNY0; -.
DR PaxDb; F4JNY0; -.
DR ProteomicsDB; 244439; -. [F4JNY0-1]
DR EnsemblPlants; AT4G36050.1; AT4G36050.1; AT4G36050. [F4JNY0-2]
DR EnsemblPlants; AT4G36050.2; AT4G36050.2; AT4G36050. [F4JNY0-1]
DR GeneID; 829761; -.
DR Gramene; AT4G36050.1; AT4G36050.1; AT4G36050. [F4JNY0-2]
DR Gramene; AT4G36050.2; AT4G36050.2; AT4G36050. [F4JNY0-1]
DR KEGG; ath:AT4G36050; -.
DR Araport; AT4G36050; -.
DR TAIR; locus:2135164; AT4G36050.
DR eggNOG; KOG1294; Eukaryota.
DR HOGENOM; CLU_010374_3_0_1; -.
DR InParanoid; F4JNY0; -.
DR OMA; FIWSSDW; -.
DR OrthoDB; 1352540at2759; -.
DR PRO; PR:F4JNY0; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; F4JNY0; baseline and differential.
DR Genevisible; F4JNY0; AT.
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:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IDA:TAIR.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; IBA:GO_Central.
DR GO; GO:0046403; F:polynucleotide 3'-phosphatase activity; IDA:TAIR.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
DR GO; GO:0080111; P:DNA demethylation; IGI:TAIR.
DR GO; GO:0006281; P:DNA repair; IGI:TAIR.
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 InterPro; IPR010666; Znf_GRF.
DR PANTHER; PTHR22748; PTHR22748; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR Pfam; PF06839; zf-GRF; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; Endonuclease; Exonuclease;
KW Hydrolase; Magnesium; Metal-binding; Nuclease; Nucleus; Reference proteome;
KW Zinc; Zinc-finger.
FT CHAIN 1..610
FT /note="DNA-(apurinic or apyrimidinic site) endonuclease 2"
FT /id="PRO_0000432792"
FT ZN_FING 554..587
FT /note="GRF-type"
FT REGION 486..536
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 324
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 37
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 194
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 196
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 323
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 324
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT VAR_SEQ 1..201
FT /note="Missing (in isoform 2 and isoform 3)"
FT /id="VSP_057574"
FT VAR_SEQ 587..609
FT /note="KQTVVISNGLHQNSETSKRVMRS -> GPSSNPEANCGYFKWASSKFRD
FT (in isoform 2)"
FT /id="VSP_057575"
SQ SEQUENCE 610 AA; 67825 MW; B85E436B2EA3E73F CRC64;
MKIVTYNVNG LRQRVSQFDS LLKLLDSFDA DIICFQETKL RRQELTADLA IADGYESFFS
CTRTSEKGRT GYSGVATFCR VKSASSSCET ALPVTAEEGI TGLVNSNSRG GKSETSTVAE
GLEEYEKEEL LMIDQEGRCV ITDHGHFVVF NVYGPRAVAD DADRIEFKHR FYGVLERRWE
CLLRQGRRVF VVGDLNIAPF AMDRCEAGPD FEKNEFRKWF RSLLVERGGS FSDVFRSKHP
ERKDAFTCWS SSSGAEQFNY GSRIDHILVA GSCLHQDEDK QGHSFLACHV KECDILTEYK
RFKNENMPTR WKGGLVTKFK GSDHVPVFIS FDDLPDIPEH STPPLASRYL PMIYGFQQTL
VSVFKKRRAN EEAKAIEVSC SSSTQSNTSS ICGDISTGPL RNCGSMGISL EKSCSFENKS
TSGVTEAETV AATGSIDNLS DGIRASSVRA LNISRDGDRK KARKIQSSQL SLKSFFTTNS
KVNNVEDSSS SYVSSSPSSQ VESITEPNVS GKEDSEPTTS TQEQDQTGSS AKQKNDAALM
EWQRIQNLMQ NSIPLCKGHK EACVARVVKK PGPTFGRRFY VCSRAEKQTV VISNGLHQNS
ETSKRVMRSK
