ZDP_ARATH
ID ZDP_ARATH Reviewed; 694 AA.
AC Q84JE8; F4IXD6; Q8LL89; Q9LKB5;
DT 03-OCT-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Polynucleotide 3'-phosphatase ZDP;
DE EC=3.1.3.32;
DE AltName: Full=DNA nick sensor protein;
GN Name=ZDP; OrderedLocusNames=At3g14890; ORFNames=K15M2.3;
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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] (ISOFORM 1).
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 [MRNA] OF 48-684 (ISOFORM 2), FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND
RP DNA-BINDING.
RC STRAIN=cv. Columbia;
RX PubMed=11948185; DOI=10.1074/jbc.m201411200;
RA Petrucco S., Volpi G., Bolchi A., Rivetti C., Ottonello S.;
RT "A nick-sensing DNA 3'-repair enzyme from Arabidopsis.";
RL J. Biol. Chem. 277:23675-23683(2002).
RN [5]
RP SEQUENCE REVISION.
RA Petrucco S., Bolchi A., Volpi G.;
RL Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, INTERACTION WITH ROS1, SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=22325353; DOI=10.1016/j.molcel.2011.11.034;
RA Martinez-Macias M.I., Qian W., Miki D., Pontes O., Liu Y., Tang K., Liu R.,
RA Morales-Ruiz T., Ariza R.R., Roldan-Arjona T., Zhu J.K.;
RT "A DNA 3' phosphatase functions in active DNA demethylation in
RT Arabidopsis.";
RL Mol. Cell 45:357-370(2012).
RN [7]
RP INTERACTION WITH XRCC1, AND ACTIVITY REGULATION.
RX PubMed=23316050; DOI=10.1074/jbc.m112.427617;
RA Martinez-Macias M.I., Cordoba-Canero D., Ariza R.R., Roldan-Arjona T.;
RT "The DNA repair protein XRCC1 functions in the plant DNA demethylation
RT pathway by stimulating cytosine methylation (5-meC) excision, gap
RT tailoring, and DNA ligation.";
RL J. Biol. Chem. 288:5496-5505(2013).
RN [8]
RP 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: Nick-sensing 3'-phosphoesterase involved in a base excision
CC repair pathway required for active DNA demethylation. The N-terminal
CC DNA-binding domain binds specifically to gap sites and sharply bends
CC the target DNA. Lacks 5'-kinase activity but is capable of 3'-
CC phosphoglycolate end processing. Inactive on 3'-alpha,beta-unsaturated
CC aldehyde (3'-dRP). Protects partially genes from transcriptional
CC silencing by preventing promoter DNA hypermethylation.
CC {ECO:0000269|PubMed:11948185, ECO:0000269|PubMed:22325353}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'end (2'-deoxyribonucleotide 3'-phosphate)-DNA + H2O = a
CC 3'-end 2'-deoxyribonucleotide-DNA + phosphate; Xref=Rhea:RHEA:14113,
CC Rhea:RHEA-COMP:13863, Rhea:RHEA-COMP:13864, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:138147, ChEBI:CHEBI:138148;
CC EC=3.1.3.32; Evidence={ECO:0000269|PubMed:11948185};
CC -!- ACTIVITY REGULATION: Activated by the presence of DNA
CC (PubMed:11948185). Stimulated by XRCC1 (PubMed:23316050).
CC {ECO:0000269|PubMed:11948185, ECO:0000269|PubMed:23316050}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=22 uM for single-stranded oligonucleotide
CC {ECO:0000269|PubMed:11948185};
CC KM=35 uM for double-stranded oligonucleotide
CC {ECO:0000269|PubMed:11948185};
CC Vmax=35 pmol/min/pmol enzyme with single-stranded oligonucleotide as
CC substrate {ECO:0000269|PubMed:11948185};
CC Vmax=46 pmol/min/pmol enzyme with double-stranded oligonucleotide as
CC substrate {ECO:0000269|PubMed:11948185};
CC -!- SUBUNIT: Interacts with ROS1 (via the central region)
CC (PubMed:22325353). Binds to XRCC1 (PubMed:23316050).
CC {ECO:0000269|PubMed:22325353, ECO:0000269|PubMed:23316050}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:22325353}. Note=Not found in the nucleolus
CC (PubMed:22325353). Co-localizes in nucleoplasmic foci with APE1L and
CC ROS1, two components of the DNA demethylase machinery
CC (PubMed:25569774). {ECO:0000269|PubMed:22325353,
CC ECO:0000269|PubMed:25569774}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q84JE8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q84JE8-2; Sequence=VSP_044164;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions (PubMed:22325353, PubMed:25569774). Loss of 3'-phosphatase
CC activity and hypersensitivity to DNA-damaging agents (PubMed:22325353).
CC Increased DNA methylation and transcriptional gene silencing
CC (PubMed:22325353). 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:22325353,
CC ECO:0000269|PubMed:25569774}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the DNA 3'
CC phosphatase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA97052.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP000370; BAA97052.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE75584.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75585.1; -; Genomic_DNA.
DR EMBL; BT003865; AAO41914.1; -; mRNA.
DR EMBL; BT005159; AAO50692.1; -; mRNA.
DR EMBL; AF453835; AAM69280.2; -; mRNA.
DR RefSeq; NP_188107.3; NM_112351.4. [Q84JE8-1]
DR RefSeq; NP_850586.2; NM_180255.3. [Q84JE8-2]
DR AlphaFoldDB; Q84JE8; -.
DR SMR; Q84JE8; -.
DR BioGRID; 6052; 2.
DR STRING; 3702.AT3G14890.1; -.
DR iPTMnet; Q84JE8; -.
DR PaxDb; Q84JE8; -.
DR PRIDE; Q84JE8; -.
DR ProteomicsDB; 232325; -. [Q84JE8-1]
DR EnsemblPlants; AT3G14890.1; AT3G14890.1; AT3G14890. [Q84JE8-1]
DR EnsemblPlants; AT3G14890.2; AT3G14890.2; AT3G14890. [Q84JE8-2]
DR GeneID; 820718; -.
DR Gramene; AT3G14890.1; AT3G14890.1; AT3G14890. [Q84JE8-1]
DR Gramene; AT3G14890.2; AT3G14890.2; AT3G14890. [Q84JE8-2]
DR KEGG; ath:AT3G14890; -.
DR Araport; AT3G14890; -.
DR TAIR; locus:2086355; AT3G14890.
DR eggNOG; KOG1037; Eukaryota.
DR eggNOG; KOG2134; Eukaryota.
DR OMA; PKTGMWN; -.
DR OrthoDB; 540341at2759; -.
DR PhylomeDB; Q84JE8; -.
DR BioCyc; ARA:AT3G14890-MON; -.
DR BRENDA; 3.1.3.32; 399.
DR BRENDA; 3.1.3.7; 399.
DR PRO; PR:Q84JE8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q84JE8; baseline and differential.
DR Genevisible; Q84JE8; AT.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003690; F:double-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0046404; F:polydeoxyribonucleotide 5'-hydroxyl-kinase activity; IBA:GO_Central.
DR GO; GO:0046403; F:polynucleotide 3'-phosphatase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0080111; P:DNA demethylation; IGI:TAIR.
DR GO; GO:0006281; P:DNA repair; IGI:TAIR.
DR GO; GO:0046939; P:nucleotide phosphorylation; IBA:GO_Central.
DR Gene3D; 3.30.1740.10; -; 3.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006549; HAD-SF_hydro_IIIA.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR013954; PNK3P.
DR InterPro; IPR006551; Polynucleotide_phosphatase.
DR InterPro; IPR001510; Znf_PARP.
DR InterPro; IPR036957; Znf_PARP_sf.
DR Pfam; PF08645; PNK3P; 1.
DR Pfam; PF00645; zf-PARP; 3.
DR SMART; SM01336; zf-PARP; 3.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01664; DNA-3'-Pase; 1.
DR TIGRFAMs; TIGR01662; HAD-SF-IIIA; 1.
DR PROSITE; PS50064; PARP_ZN_FINGER_2; 3.
PE 1: Evidence at protein level;
KW Alternative splicing; DNA damage; DNA repair; DNA-binding; Hydrolase;
KW Metal-binding; Nucleus; Reference proteome; Repeat; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..694
FT /note="Polynucleotide 3'-phosphatase ZDP"
FT /id="PRO_0000419433"
FT ZN_FING 50..132
FT /note="PARP-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00264"
FT ZN_FING 165..247
FT /note="PARP-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00264"
FT ZN_FING 328..410
FT /note="PARP-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00264"
FT REGION 266..331
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 291..324
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 245..254
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11948185"
FT /id="VSP_044164"
FT CONFLICT 660
FT /note="K -> E (in Ref. 4; AAM69280)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 694 AA; 77387 MW; C49E53DA71F96AE8 CRC64;
MITVAPFVSL RFQFPLYIIN RSTLFFRERT QYLVYNTCHI LRTTAKTMPV VAEYAKSNRS
SCRSCSNKIA VKSLRLGLIS KGRGGVDMTR WHHFDCFPTD SESIASVDDI QGLSALEKED
QDALTKLVEQ CGKVPAKKPD EKKGKAKKHI MGPKGLTKAA TSSKVIADNA KSSRSSCNRC
SQTIVSKDLR VGLVTEDSRG FDITRWHHLG CFPIDFHPID SVEDIGGYSS LEKGDQMELK
YLAEVNKKDK TLIDDVQKMD EGDDEAIADN ELTEETKKGK HSPVAKLVEQ PGEPAKEDED
EESKKPASDE ISEQKTKDVK NSPDSSKVIS EYAKSSRSTC KKCSQTIAAK ELRLGLVTRN
FRGFDMKQWH HLGCFPVDSD PIVSVEDIGG FSELQSGDQD ALKELVQQCG KQTLVDKMDE
DNDDTEAKIK LTEETNKRKH SEVGEMVEED ESLTKAKQQM AKTHKVNMSE STSQVEVEAE
ITLSASDVKD KYRDANLLPK WKAFETVIFL ERDDGLNDSE KIAAFDFDGC LAKTSVKIVG
ADAWSLMYPS IPEKLQSLHD QGYKLVIFTN ESNIDRWKNK RQAAVDSKIG RLNSFIERVK
VPIQVFIACG VSSSGGKGGK DDLYRKPKAG MWQLMKKHFN SGIAIDMDKS FYVGDAAGRK
MDHSDADIKF AQASGLKFFT PEEYFIPSST SPGT
