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DNA-(apurinic or apyrimidinic site) lyase, chloroplastic (EC 4.2.99.18) (Apurinic endonuclease-redox protein)

 ARP_ARATH               Reviewed;         536 AA.
P45951;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
30-MAY-2000, sequence version 2.
23-MAY-2018, entry version 154.
RecName: Full=DNA-(apurinic or apyrimidinic site) lyase, chloroplastic {ECO:0000303|PubMed:7512729};
EC=4.2.99.18 {ECO:0000255|PROSITE-ProRule:PRU00764};
AltName: Full=Apurinic endonuclease-redox protein;
Name=ARP {ECO:0000303|PubMed:7512729}; Synonyms=REF;
OrderedLocusNames=At2g41460 {ECO:0000312|Araport:AT2G41460};
ORFNames=T26J13.5 {ECO:0000312|EMBL:AAC23731.1};
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=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[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 [MRNA] OF 10-536, FUNCTION, AND TISSUE
SPECIFICITY.
STRAIN=cv. Columbia; TISSUE=Callus;
PubMed=7512729; DOI=10.1073/pnas.91.8.3299;
Babiychuk E., Kushnir S., van Montagu M., Inze D.;
"The Arabidopsis thaliana apurinic endonuclease Arp reduces human
transcription factors Fos and Jun.";
Proc. Natl. Acad. Sci. U.S.A. 91:3299-3303(1994).
[4]
FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=19372224; DOI=10.1074/jbc.M109.008342;
Gutman B.L., Niyogi K.K.;
"Evidence for base excision repair of oxidative DNA damage in
chloroplasts of Arabidopsis thaliana.";
J. Biol. Chem. 284:17006-17012(2009).
[5]
FUNCTION, MUTAGENESIS OF ARG-354, 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).
[6]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21781197; DOI=10.1111/j.1365-313X.2011.04720.x;
Cordoba-Canero D., Roldan-Arjona T., Ariza R.R.;
"Arabidopsis ARP endonuclease functions in a branched base excision
DNA repair pathway completed by LIG1.";
Plant J. 68:693-702(2011).
[7]
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).
[8]
FUNCTION, CATALYTIC ACTIVITY, 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: Repairs oxidative DNA damages, seems also to act as a
redox factor (PubMed:7512729). Is multifunctional and may be
involved both in DNA repair and in the regulation of transcription
(PubMed:7512729). Exhibits apurinic/apyrimidinic (AP) endonuclease
activity (PubMed:25569774, PubMed:21781197, PubMed:25228464).
Catalyzes the conversion of 3'-phosphor-alpha,beta-unsaturated
aldehyde (3'-PUA) to 3'-OH (PubMed:25228464). May be involved in
base excision repair in chloroplasts (PubMed:19372224). According
to a report, has a significant in vitro 3'-phosphatase activity
(PubMed:25228464). According to another report, has no in vitro
3'-phosphatase activity (PubMed:25569774). Has a strong non-
specific affinity to DNA (PubMed:25228464).
{ECO:0000269|PubMed:19372224, ECO:0000269|PubMed:21781197,
ECO:0000269|PubMed:25228464, ECO:0000269|PubMed:25569774,
ECO:0000269|PubMed:7512729, ECO:0000305|PubMed:19172180}.
-!- 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};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000250|UniProtKB:P27695};
Note=Probably binds two magnesium or manganese ions per subunit.
{ECO:0000250|UniProtKB:P27695};
-!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma, chloroplast
nucleoid {ECO:0000269|PubMed:19372224}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences.;
Name=1;
IsoId=P45951-1; Sequence=Displayed;
-!- TISSUE SPECIFICITY: Expressed in the siliques, flowers, and stems
(PubMed:7512729). A high level expression is seen in the leaves
(PubMed:7512729). Expressed in both vegetative and reproductive
organs (PubMed:25228464). {ECO:0000269|PubMed:25228464,
ECO:0000269|PubMed:7512729}.
-!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:19372224,
PubMed:19172180, PubMed:21781197, PubMed:25569774). Loss of
chloroplastic glycosylase-lyase/endonuclease activity
(PubMed:19372224). Hypersensitivity to 5-fluorouracil
(PubMed:21781197). Ape1l arp double mutants have no visible
phenotype (PubMed:19172180). Ape2 arp double mutants have no
visible phenotype (PubMed:19172180). {ECO:0000269|PubMed:19172180,
ECO:0000269|PubMed:19372224, ECO:0000269|PubMed:21781197,
ECO:0000269|PubMed:25569774}.
-!- SIMILARITY: Belongs to the DNA repair enzymes AP/ExoA family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AC004625; AAC23731.1; -; Genomic_DNA.
EMBL; CP002685; AEC09984.1; -; Genomic_DNA.
EMBL; X76912; CAA54234.1; -; mRNA.
PIR; T02441; T02441.
RefSeq; NP_181677.1; NM_129709.5. [P45951-1]
UniGene; At.25567; -.
ProteinModelPortal; P45951; -.
SMR; P45951; -.
STRING; 3702.AT2G41460.1; -.
iPTMnet; P45951; -.
PaxDb; P45951; -.
PRIDE; P45951; -.
EnsemblPlants; AT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
GeneID; 818744; -.
Gramene; AT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
KEGG; ath:AT2G41460; -.
Araport; AT2G41460; -.
TAIR; locus:2060540; AT2G41460.
eggNOG; KOG1294; Eukaryota.
eggNOG; COG0708; LUCA.
InParanoid; P45951; -.
KO; K01142; -.
OMA; KKPQKDW; -.
OrthoDB; EOG09360F70; -.
PhylomeDB; P45951; -.
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:P45951; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; P45951; baseline and differential.
Genevisible; P45951; AT.
GO; GO:0042644; C:chloroplast nucleoid; IDA:TAIR.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0008408; F:3'-5' exonuclease activity; IDA:TAIR.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0003906; F:DNA-(apurinic or apyrimidinic site) endonuclease activity; IDA:TAIR.
GO; GO:0008311; F:double-stranded DNA 3'-5' exodeoxyribonuclease activity; IBA:GO_Central.
GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0016791; F:phosphatase activity; IDA:TAIR.
GO; GO:0004528; F:phosphodiesterase I activity; IDA:TAIR.
GO; GO:0006284; P:base-excision repair; IBA:GO_Central.
GO; GO:0033683; P:nucleotide-excision repair, DNA incision; IDA:TAIR.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; TAS:TAIR.
Gene3D; 1.10.720.30; -; 1.
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.
InterPro; IPR003034; SAP_dom.
InterPro; IPR036361; SAP_dom_sf.
PANTHER; PTHR22748; PTHR22748; 1.
Pfam; PF03372; Exo_endo_phos; 1.
Pfam; PF02037; SAP; 1.
SMART; SM00513; SAP; 1.
SUPFAM; SSF56219; SSF56219; 1.
SUPFAM; SSF68906; SSF68906; 1.
TIGRFAMs; TIGR00633; xth; 1.
PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
PROSITE; PS00727; AP_NUCLEASE_F1_2; 1.
PROSITE; PS00728; AP_NUCLEASE_F1_3; 1.
PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
PROSITE; PS50800; SAP; 1.
1: Evidence at protein level;
Alternative splicing; Chloroplast; Complete proteome; DNA damage;
DNA repair; Lyase; Magnesium; Metal-binding; Plastid;
Reference proteome.
CHAIN 1 536 DNA-(apurinic or apyrimidinic site)
lyase, chloroplastic.
/FTId=PRO_0000200018.
DOMAIN 97 131 SAP. {ECO:0000255|PROSITE-
ProRule:PRU00186}.
REGION 1 278 Highly charged; increases the affinity of
ARP for DNA.
REGION 279 536 AP endonuclease.
ACT_SITE 389 389 {ECO:0000250|UniProtKB:P27695}.
ACT_SITE 527 527 Proton acceptor. {ECO:0000255|PROSITE-
ProRule:PRU00764}.
METAL 282 282 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
METAL 313 313 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
METAL 429 429 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
METAL 431 431 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
METAL 526 526 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
METAL 527 527 Magnesium or manganese.
{ECO:0000255|PROSITE-ProRule:PRU00764}.
SITE 431 431 Transition state stabilizer.
{ECO:0000250|UniProtKB:P27695}.
SITE 501 501 Important for catalytic activity.
{ECO:0000250|UniProtKB:P27695}.
SITE 527 527 Interaction with DNA substrate.
{ECO:0000250|UniProtKB:P27695}.
MUTAGEN 354 354 R->W: In arp-1; loss of activity.
{ECO:0000269|PubMed:19172180}.
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


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