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Protein

DNA-(apurinic or apyrimidinic site) lyase, chloroplastic

Gene

ARP

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).1 Publication5 Publications

Catalytic activityi

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.2 Publications

Cofactori

Mg2+1 Publication, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi282 – 2821Magnesium or manganesePROSITE-ProRule annotation
Metal bindingi313 – 3131Magnesium or manganesePROSITE-ProRule annotation
Active sitei389 – 3891By similarity
Metal bindingi429 – 4291Magnesium or manganesePROSITE-ProRule annotation
Metal bindingi431 – 4311Magnesium or manganesePROSITE-ProRule annotation
Sitei431 – 4311Transition state stabilizerBy similarity
Sitei501 – 5011Important for catalytic activityBy similarity
Metal bindingi526 – 5261Magnesium or manganesePROSITE-ProRule annotation
Active sitei527 – 5271Proton acceptorPROSITE-ProRule annotation
Metal bindingi527 – 5271Magnesium or manganesePROSITE-ProRule annotation
Sitei527 – 5271Interaction with DNA substrateBy similarity

GO - Molecular functioni

  1. DNA-(apurinic or apyrimidinic site) lyase activity Source: TAIR
  2. DNA binding Source: InterPro
  3. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: GO_Central
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. base-excision repair Source: GO_Central
  2. nucleic acid phosphodiester bond hydrolysis Source: GOC
  3. positive regulation of transcription, DNA-templated Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciARA:AT2G41460-MONOMER.
ARA:GQT-950-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase, chloroplastic1 Publication (EC:4.2.99.18PROSITE-ProRule annotation)
Alternative name(s):
Apurinic endonuclease-redox protein
Gene namesi
Name:ARP1 Publication
Synonyms:REF
Ordered Locus Names:At2g41460Imported
ORF Names:T26J13.5Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G41460.

Subcellular locationi

  1. Plastidchloroplast stromachloroplast nucleoid 1 Publication

GO - Cellular componenti

  1. chloroplast nucleoid Source: TAIR
  2. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Disruption phenotypei

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).4 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi354 – 3541R → W in arp-1; loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 536536DNA-(apurinic or apyrimidinic site) lyase, chloroplasticPRO_0000200018Add
BLAST

Proteomic databases

PaxDbiP45951.
PRIDEiP45951.

Expressioni

Tissue specificityi

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).2 Publications

Gene expression databases

ExpressionAtlasiP45951. baseline and differential.
GenevestigatoriP45951.

Structurei

3D structure databases

ProteinModelPortaliP45951.
SMRiP45951. Positions 241-536.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini97 – 13135SAPPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 278278Highly charged; increases the affinity of ARP for DNAAdd
BLAST
Regioni279 – 536258AP endonucleaseAdd
BLAST

Sequence similaritiesi

Belongs to the DNA repair enzymes AP/ExoA family.Curated
Contains 1 SAP domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0708.
InParanoidiP45951.
KOiK01142.
OMAiQRENFDI.
PhylomeDBiP45951.

Family and domain databases

Gene3Di1.10.720.30. 1 hit.
3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
IPR003034. SAP_dom.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
PF02037. SAP. 1 hit.
[Graphical view]
SMARTiSM00513. SAP. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
PS50800. SAP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: P45951-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MNNVLQFGLQ SSAIYVAKFL VVPLRSLRVG SSFVGVGVGT RSFNKRLMSN
60 70 80 90 100
ATAFSINNSK RKELKIPGAA IDQNCHQMGS DTDRDEMGTL QDDRKEIEAM
110 120 130 140 150
TVQELRSTLR KLGVPVKGRK QELISTLRLH MDSNLPDQKE TSSSTRSDSV
160 170 180 190 200
TIKRKISNRE EPTEDECTNS EAYDIEHGEK RVKQSTEKNL KAKVSAKAIA
210 220 230 240 250
KEQKSLMRTG KQQIQSKEET SSTISSELLK TEEIISSPSQ SEPWTVLAHK
260 270 280 290 300
KPQKDWKAYN PKTMRPPPLP EGTKCVKVMT WNVNGLRGLL KFESFSALQL
310 320 330 340 350
AQRENFDILC LQETKLQVKD VEEIKKTLID GYDHSFWSCS VSKLGYSGTA
360 370 380 390 400
IISRIKPLSV RYGTGLSGHD TEGRIVTAEF DSFYLINTYV PNSGDGLKRL
410 420 430 440 450
SYRIEEWDRT LSNHIKELEK SKPVVLTGDL NCAHEEIDIF NPAGNKRSAG
460 470 480 490 500
FTIEERQSFG ANLLDKGFVD TFRKQHPGVV GYTYWGYRHG GRKTNKGWRL
510 520 530
DYFLVSQSIA ANVHDSYILP DINGSDHCPI GLILKL
Length:536
Mass (Da):60,260
Last modified:May 30, 2000 - v2
Checksum:i5C1FC17EA991D27B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC004625 Genomic DNA. Translation: AAC23731.1.
CP002685 Genomic DNA. Translation: AEC09984.1.
X76912 mRNA. Translation: CAA54234.1.
PIRiT02441.
RefSeqiNP_181677.1. NM_129709.4. [P45951-1]
UniGeneiAt.25567.

Genome annotation databases

EnsemblPlantsiAT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
GeneIDi818744.
KEGGiath:AT2G41460.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC004625 Genomic DNA. Translation: AAC23731.1.
CP002685 Genomic DNA. Translation: AEC09984.1.
X76912 mRNA. Translation: CAA54234.1.
PIRiT02441.
RefSeqiNP_181677.1. NM_129709.4. [P45951-1]
UniGeneiAt.25567.

3D structure databases

ProteinModelPortaliP45951.
SMRiP45951. Positions 241-536.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PaxDbiP45951.
PRIDEiP45951.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G41460.1; AT2G41460.1; AT2G41460. [P45951-1]
GeneIDi818744.
KEGGiath:AT2G41460.

Organism-specific databases

TAIRiAT2G41460.

Phylogenomic databases

eggNOGiCOG0708.
InParanoidiP45951.
KOiK01142.
OMAiQRENFDI.
PhylomeDBiP45951.

Enzyme and pathway databases

BioCyciARA:AT2G41460-MONOMER.
ARA:GQT-950-MONOMER.

Miscellaneous databases

PROiP45951.

Gene expression databases

ExpressionAtlasiP45951. baseline and differential.
GenevestigatoriP45951.

Family and domain databases

Gene3Di1.10.720.30. 1 hit.
3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
IPR003034. SAP_dom.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
PF02037. SAP. 1 hit.
[Graphical view]
SMARTiSM00513. SAP. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
PS50800. SAP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "The Arabidopsis thaliana apurinic endonuclease Arp reduces human transcription factors Fos and Jun."
    Babiychuk E., Kushnir S., van Montagu M., Inze D.
    Proc. Natl. Acad. Sci. U.S.A. 91:3299-3303(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 10-536, FUNCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
    Tissue: Callus.
  4. "Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana."
    Gutman B.L., Niyogi K.K.
    J. Biol. Chem. 284:17006-17012(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
  5. "Requirement for abasic endonuclease gene homologues in Arabidopsis seed development."
    Murphy T.M., Belmonte M., Shu S., Britt A.B., Hatteroth J.
    PLoS ONE 4:E4297-E4297(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF ARG-354, DISRUPTION PHENOTYPE.
  6. "Arabidopsis ARP endonuclease functions in a branched base excision DNA repair pathway completed by LIG1."
    Cordoba-Canero D., Roldan-Arjona T., Ariza R.R.
    Plant J. 68:693-702(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  7. "AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis."
    Lee J., Jang H., Shin H., Choi W.L., Mok Y.G., Huh J.H.
    Nucleic Acids Res. 42:11408-11418(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, CATALYTIC ACTIVITY, COFACTOR, DNA-BINDING.
  8. "An AP endonuclease functions in active DNA dimethylation and gene imprinting in Arabidopsis."
    Li Y., Cordoba-Canero D., Qian W., Zhu X., Tang K., Zhang H., Ariza R.R., Roldan-Arjona T., Zhu J.K.
    PLoS Genet. 11:E1004905-E1004905(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiARP_ARATH
AccessioniPrimary (citable) accession number: P45951
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: May 30, 2000
Last modified: April 29, 2015
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.