ARP_ARATH
ID ARP_ARATH Reviewed; 536 AA.
AC P45951;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 2.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic {ECO:0000303|PubMed:7512729};
DE EC=3.1.11.2 {ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774};
DE AltName: Full=Apurinic endonuclease-redox protein;
GN Name=ARP {ECO:0000303|PubMed:7512729}; Synonyms=REF;
GN OrderedLocusNames=At2g41460 {ECO:0000312|Araport:AT2G41460};
GN ORFNames=T26J13.5 {ECO:0000312|EMBL:AAC23731.1};
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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 [MRNA] OF 10-536, FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia; TISSUE=Callus;
RX PubMed=7512729; DOI=10.1073/pnas.91.8.3299;
RA Babiychuk E., Kushnir S., van Montagu M., Inze D.;
RT "The Arabidopsis thaliana apurinic endonuclease Arp reduces human
RT transcription factors Fos and Jun.";
RL Proc. Natl. Acad. Sci. U.S.A. 91:3299-3303(1994).
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=19372224; DOI=10.1074/jbc.m109.008342;
RA Gutman B.L., Niyogi K.K.;
RT "Evidence for base excision repair of oxidative DNA damage in chloroplasts
RT of Arabidopsis thaliana.";
RL J. Biol. Chem. 284:17006-17012(2009).
RN [5]
RP FUNCTION, MUTAGENESIS OF ARG-354, 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, AND DISRUPTION PHENOTYPE.
RX PubMed=21781197; DOI=10.1111/j.1365-313x.2011.04720.x;
RA Cordoba-Canero D., Roldan-Arjona T., Ariza R.R.;
RT "Arabidopsis ARP endonuclease functions in a branched base excision DNA
RT repair pathway completed by LIG1.";
RL Plant J. 68:693-702(2011).
RN [7]
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 [8]
RP FUNCTION, CATALYTIC ACTIVITY, 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: Repairs oxidative DNA damages, seems also to act as a redox
CC factor (PubMed:7512729). Is multifunctional and may be involved both in
CC DNA repair and in the regulation of transcription (PubMed:7512729).
CC Exhibits apurinic/apyrimidinic (AP) endonuclease activity
CC (PubMed:25569774, PubMed:21781197, PubMed:25228464). Catalyzes the
CC conversion of 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) to
CC 3'-OH (PubMed:25228464). May be involved in base excision repair in
CC chloroplasts (PubMed:19372224). According to a report, has a
CC significant in vitro 3'-phosphatase activity (PubMed:25228464).
CC According to another report, has no in vitro 3'-phosphatase activity
CC (PubMed:25569774). Has a strong non-specific affinity to DNA
CC (PubMed:25228464). {ECO:0000269|PubMed:19372224,
CC ECO:0000269|PubMed:21781197, ECO:0000269|PubMed:25228464,
CC ECO:0000269|PubMed:25569774, ECO:0000269|PubMed:7512729,
CC ECO:0000305|PubMed:19172180}.
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: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: Plastid, chloroplast stroma, chloroplast nucleoid
CC {ECO:0000269|PubMed:19372224}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=P45951-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in the siliques, flowers, and stems
CC (PubMed:7512729). A high level expression is seen in the leaves
CC (PubMed:7512729). Expressed in both vegetative and reproductive organs
CC (PubMed:25228464). {ECO:0000269|PubMed:25228464,
CC ECO:0000269|PubMed:7512729}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:19372224,
CC PubMed:19172180, PubMed:21781197, PubMed:25569774). Loss of
CC chloroplastic glycosylase-lyase/endonuclease activity
CC (PubMed:19372224). Hypersensitivity to 5-fluorouracil
CC (PubMed:21781197). Ape1l arp double mutants have no visible phenotype
CC (PubMed:19172180). Ape2 arp double mutants have no visible phenotype
CC (PubMed:19172180). {ECO:0000269|PubMed:19172180,
CC ECO:0000269|PubMed:19372224, ECO:0000269|PubMed:21781197,
CC ECO:0000269|PubMed:25569774}.
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC004625; AAC23731.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09984.1; -; Genomic_DNA.
DR EMBL; X76912; CAA54234.1; -; mRNA.
DR PIR; T02441; T02441.
DR RefSeq; NP_181677.1; NM_129709.5. [P45951-1]
DR AlphaFoldDB; P45951; -.
DR SMR; P45951; -.
DR STRING; 3702.AT2G41460.1; -.
DR iPTMnet; P45951; -.
DR PaxDb; P45951; -.
DR PRIDE; P45951; -.
DR ProteomicsDB; 246925; -. [P45951-1]
DR EnsemblPlants; AT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
DR GeneID; 818744; -.
DR Gramene; AT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
DR KEGG; ath:AT2G41460; -.
DR Araport; AT2G41460; -.
DR TAIR; locus:2060540; AT2G41460.
DR eggNOG; KOG1294; Eukaryota.
DR HOGENOM; CLU_027539_5_1_1; -.
DR InParanoid; P45951; -.
DR PhylomeDB; P45951; -.
DR PRO; PR:P45951; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; P45951; baseline and differential.
DR Genevisible; P45951; AT.
DR GO; GO:0042644; C:chloroplast nucleoid; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:TAIR.
DR GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016791; F:phosphatase activity; IDA:TAIR.
DR GO; GO:0004528; F:phosphodiesterase I activity; IDA:TAIR.
DR GO; GO:0008081; F:phosphoric diester hydrolase activity; IBA:GO_Central.
DR GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
DR GO; GO:0033683; P:nucleotide-excision repair, DNA incision; IDA:TAIR.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; TAS:TAIR.
DR Gene3D; 1.10.720.30; -; 1.
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 InterPro; IPR003034; SAP_dom.
DR InterPro; IPR036361; SAP_dom_sf.
DR PANTHER; PTHR22748; PTHR22748; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR Pfam; PF02037; SAP; 1.
DR SMART; SM00513; SAP; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
DR SUPFAM; SSF68906; SSF68906; 1.
DR TIGRFAMs; TIGR00633; xth; 1.
DR PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR PROSITE; PS00727; AP_NUCLEASE_F1_2; 1.
DR PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
DR PROSITE; PS50800; SAP; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; DNA damage; DNA repair; Hydrolase;
KW Magnesium; Metal-binding; Plastid; Reference proteome.
FT CHAIN 1..536
FT /note="DNA-(apurinic or apyrimidinic site) endonuclease,
FT chloroplastic"
FT /id="PRO_0000200018"
FT DOMAIN 97..131
FT /note="SAP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00186"
FT REGION 1..278
FT /note="Highly charged; increases the affinity of ARP for
FT DNA"
FT REGION 129..168
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 203..225
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 279..536
FT /note="AP endonuclease"
FT COMPBIAS 129..151
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 152..168
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 206..225
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 389
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT ACT_SITE 527
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 282
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 313
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 429
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 431
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 526
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT BINDING 527
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00764"
FT SITE 431
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT SITE 501
FT /note="Important for catalytic activity"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT SITE 527
FT /note="Interaction with DNA substrate"
FT /evidence="ECO:0000250|UniProtKB:P27695"
FT MUTAGEN 354
FT /note="R->W: In arp-1; loss of activity."
FT /evidence="ECO:0000269|PubMed:19172180"
SQ SEQUENCE 536 AA; 60260 MW; 5C1FC17EA991D27B CRC64;
MNNVLQFGLQ SSAIYVAKFL VVPLRSLRVG SSFVGVGVGT RSFNKRLMSN ATAFSINNSK
RKELKIPGAA IDQNCHQMGS DTDRDEMGTL QDDRKEIEAM TVQELRSTLR KLGVPVKGRK
QELISTLRLH MDSNLPDQKE TSSSTRSDSV TIKRKISNRE EPTEDECTNS EAYDIEHGEK
RVKQSTEKNL KAKVSAKAIA KEQKSLMRTG KQQIQSKEET SSTISSELLK TEEIISSPSQ
SEPWTVLAHK KPQKDWKAYN PKTMRPPPLP EGTKCVKVMT WNVNGLRGLL KFESFSALQL
AQRENFDILC LQETKLQVKD VEEIKKTLID GYDHSFWSCS VSKLGYSGTA IISRIKPLSV
RYGTGLSGHD TEGRIVTAEF DSFYLINTYV PNSGDGLKRL SYRIEEWDRT LSNHIKELEK
SKPVVLTGDL NCAHEEIDIF NPAGNKRSAG FTIEERQSFG ANLLDKGFVD TFRKQHPGVV
GYTYWGYRHG GRKTNKGWRL DYFLVSQSIA ANVHDSYILP DINGSDHCPI GLILKL
