Protein: Polynucleotide 3'-phosphatase ZDP (EC 3.1.3.32) (DNA nick sensor protein) (Q84JE8)
Organism: Arabidopsis thaliana (Mouse-ear cress)
Function: Nick-sensing 3'-phosphoesterase involved in a base excision repair pathway required for active DNA demethylation. The N-terminal DNA-binding domain binds specifically to gap sites and sharply bends the target DNA. Lacks 5'-kinase activity but is capable of 3'-phosphoglycolate end processing. Inactive on 3'-alpha,beta-unsaturated aldehyde (3'-dRP). Protects partially genes from transcriptional silencing by preventing promoter DNA hypermethylation.
Subcellular location: Nucleus, nucleoplasm {ECO:0000269|PubMed:22325353}. Note=Not found in the nucleolus (PubMed:22325353). Co-localizes in nucleoplasmic foci with APE1L and ROS1, two components of the DNA demethylase machinery (PubMed:25569774). {ECO:0000269|PubMed:22325353, ECO:0000269|PubMed:25569774}.
Sequence: MITVAPFVSLRFQFPLYIINRSTLFFRERTQYLVYNTCHILRTTAKTMPVVAEYAKSNRSSCRSCSNKIAVKSLRLGLISKGRGGVDMTRWHHFDCFPTDSESIASVDDIQGLSALEKEDQDALTKLVEQCGKVPAKKPDEKKGKAKKHIMGPKGLTKAATSSKVIADNAKSSRSSCNRCSQTIVSKDLRVGLVTEDSRGFDITRWHHLGCFPIDFHPIDSVEDIGGYSSLEKGDQMELKYLAEVNKKDKTLIDDVQKMDEGDDEAIADNELTEETKKGKHSPVAKLVEQPGEPAKEDEDEESKKPASDEISEQKTKDVKNSPDSSKVISEYAKSSRSTCKKCSQTIAAKELRLGLVTRNFRGFDMKQWHHLGCFPVDSDPIVSVEDIGGFSELQSGDQDALKELVQQCGKQTLVDKMDEDNDDTEAKIKLTEETNKRKHSEVGEMVEEDESLTKAKQQMAKTHKVNMSESTSQVEVEAEITLSASDVKDKYRDANLLPKWKAFETVIFLERDDGLNDSEKIAAFDFDGCLAKTSVKIVGADAWSLMYPSIPEKLQSLHDQGYKLVIFTNESNIDRWKNKRQAAVDSKIGRLNSFIERVKVPIQVFIACGVSSSGGKGGKDDLYRKPKAGMWQLMKKHFNSGIAIDMDKSFYVGDAAGRKMDHSDADIKFAQASGLKFFTPEEYFIPSSTSPGT
InterPro domains: - IPR013954: Polynucleotide kinase 3 phosphatase (family) [521-685]
- IPR001510: Zinc finger, PARP-type (domain) [50-410]
- IPR036412: HAD-like superfamily (homologous_superfamily) [519-687]
- IPR023214: HAD superfamily (homologous_superfamily) [499-692]
- IPR006551: Polynucleotide 3'-phosphatase (domain) [509-685]
- IPR036957: Zinc finger, PARP-type superfamily (homologous_superfamily) [42-430]
- IPR006549: HAD-superfamily hydrolase,subfamily IIIA (domain) [521-679]
Interaction partners: - DNA-repair protein XRCC1
- DNA polymerase lambda
- DNA ligase 1
- DNA-
- DNA ligase 6
- ATP-dependent DNA helicase 2 subunit KU70
- ATP-dependent DNA helicase 2 subunit KU80
- DNA ligase 4
- DNA-
- DNA ligase
Gene Ontology annotations:
Molecular Function (MF): GO:0003674 (molecular function), GO:0003824 (catalytic activity), GO:0140640 (catalytic activity, acting on a nucleic acid), GO:0016787 (hydrolase activity), GO:0016788 (hydrolase activity, acting on ester bonds), GO:0140097 (catalytic activity, acting on DNA), GO:0004518 (nuclease activity), GO:0004536 (deoxyribonuclease activity), GO:0004520 (DNA endonuclease activity), GO:0004519 (endonuclease activity)
Biological Process (BP): GO:0008150 (biological process), GO:0008152 (metabolic process), GO:0009987 (cellular process), GO:0050896 (response to stimulus), GO:0051716 (cellular response to stimulus), GO:0009628 (response to abiotic stimulus), GO:0006950 (response to stress), GO:0044237 (cellular metabolic process), GO:0071704 (organic substance metabolic process), GO:0044238 (primary metabolic process), GO:0006807 (nitrogen compound metabolic process), GO:0006725 (cellular aromatic compound metabolic process), GO:1901360 (organic cyclic compound metabolic process), GO:0034641 (cellular nitrogen compound metabolic process), GO:0006139 (nucleobase-containing compound metabolic process), GO:0044260 (cellular macromolecule metabolic process), GO:0043170 (macromolecule metabolic process), GO:0046483 (heterocycle metabolic process), GO:0009314 (response to radiation), GO:0033554 (cellular response to stress), GO:0006259 (DNA metabolic process), GO:0009416 (response to light stimulus), GO:0090304 (nucleic acid metabolic process), GO:0006974 (cellular response to DNA damage stimulus), GO:0006281 (DNA repair), GO:0009411 (response to UV), GO:0010224 (response to UV-B)
Cellular Component (CC): GO:0005575 (cellular component), GO:0110165 (cellular anatomical entity), GO:0005622 (intracellular anatomical structure), GO:0043226 (organelle), GO:0005737 (cytoplasm), GO:0043229 (intracellular organelle), GO:0005739 (mitochondrion), GO:0043227 (membrane-bounded organelle), GO:0043231 (intracellular membrane-bounded organelle), GO:0005634 (nucleus)