UniProtKB - A0MTA1 (APEX1_DANRE)
Protein
DNA-(apurinic or apyrimidinic site) endonuclease
Gene
apex1
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Functioni
Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Required for passage through the midblastula transition MBT. May also act as an endoribonuclease involved in the control of single-stranded RNA metabolism. Has no redox activity. Binds DNA and RNA.2 Publications
Cofactori
Mg2+By similarity, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 63 | Magnesium 1By similarity | 1 | |
Metal bindingi | 89 | Magnesium 1By similarity | 1 | |
Active sitei | 164 | By similarity | 1 | |
Active sitei | 203 | Proton donor/acceptorBy similarity | 1 | |
Metal bindingi | 203 | Magnesium 2By similarity | 1 | |
Metal bindingi | 205 | Magnesium 2By similarity | 1 | |
Sitei | 205 | Transition state stabilizerBy similarity | 1 | |
Sitei | 275 | Important for catalytic activityBy similarity | 1 | |
Metal bindingi | 300 | Magnesium 1By similarity | 1 |
GO - Molecular functioni
- DNA-(apurinic or apyrimidinic site) endonuclease activity Source: GO_Central
- DNA binding Source: UniProtKB-KW
- double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: GO_Central
- endonuclease activity Source: UniProtKB-KW
- metal ion binding Source: UniProtKB-KW
- phosphodiesterase I activity Source: GO_Central
- RNA binding Source: UniProtKB-KW
GO - Biological processi
- base-excision repair Source: GO_Central
- DNA demethylation Source: UniProtKB
- heart contraction Source: ZFIN
- heart looping Source: ZFIN
- negative regulation of apoptotic process Source: ZFIN
- oxidation-reduction process Source: GOC
- positive regulation of gene expression Source: ZFIN
Keywordsi
Molecular function | DNA-binding, Endonuclease, Hydrolase, Nuclease, RNA-binding |
Biological process | DNA damage, DNA repair |
Ligand | Magnesium, Metal-binding |
Enzyme and pathway databases
Reactomei | R-DRE-110357, Displacement of DNA glycosylase by APEX1 R-DRE-110362, POLB-Dependent Long Patch Base Excision Repair R-DRE-110373, Resolution of AP sites via the multiple-nucleotide patch replacement pathway R-DRE-5651801, PCNA-Dependent Long Patch Base Excision Repair R-DRE-73930, Abasic sugar-phosphate removal via the single-nucleotide replacement pathway R-DRE-73933, Resolution of Abasic Sites (AP sites) |
Names & Taxonomyi
Protein namesi | Recommended name: DNA-(apurinic or apyrimidinic site) endonuclease (EC:3.1.-.-)Alternative name(s): APEX nuclease Short name: APEN Apurinic-apyrimidinic endonuclease 1 Short name: AP endonuclease 1 Short name: zAP1 |
Gene namesi | Name:apex1 Synonyms:apex1a, apex1b ORF Names:si:ch211-214j24.12, zgc:66204 |
Organismi | Danio rerio (Zebrafish) (Brachydanio rerio) |
Taxonomic identifieri | 7955 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Danionidae › Danioninae › Danio |
Proteomesi |
|
Organism-specific databases
ZFINi | ZDB-GENE-040426-2761, apex1 |
Subcellular locationi
Endoplasmic reticulum
- Endoplasmic reticulum By similarity
Mitochondrion
- Mitochondrion By similarity
Nucleus
- Nucleus PROSITE-ProRule annotation
- nucleolus By similarity
- Nucleus speckle PROSITE-ProRule annotation
Other locations
- Cytoplasm PROSITE-ProRule annotation
Endoplasmic reticulum
- endoplasmic reticulum Source: UniProtKB-SubCell
Mitochondrion
- mitochondrion Source: UniProtKB-SubCell
Nucleus
- nuclear speck Source: UniProtKB-SubCell
- nucleolus Source: UniProtKB-SubCell
- nucleus Source: GO_Central
Keywords - Cellular componenti
Cytoplasm, Endoplasmic reticulum, Mitochondrion, NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 58 | T → C: Confers redox activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000402575 | 1 – 310 | DNA-(apurinic or apyrimidinic site) endonucleaseAdd BLAST | 310 |
Proteomic databases
PaxDbi | A0MTA1 |
PeptideAtlasi | A0MTA1 |
PRIDEi | A0MTA1 |
Expressioni
Developmental stagei
Expressed in unfertilized eggs and embryos at two stages (at protein level). Expressed throughout embryogenesis.1 Publication
Interactioni
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 301 | Interaction with DNA substrateBy similarity | 1 |
Protein-protein interaction databases
STRINGi | 7955.ENSDARP00000067373 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | A0MTA1 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | A0MTA1 |
Family & Domainsi
Sequence similaritiesi
Belongs to the DNA repair enzymes AP/ExoA family.Curated
Phylogenomic databases
eggNOGi | KOG1294, Eukaryota |
InParanoidi | A0MTA1 |
PhylomeDBi | A0MTA1 |
TreeFami | TF315048 |
Family and domain databases
Gene3Di | 3.60.10.10, 1 hit |
InterProi | View protein in InterPro IPR004808, AP_endonuc_1 IPR020847, AP_endonuclease_F1_BS IPR020848, AP_endonuclease_F1_CS IPR036691, Endo/exonu/phosph_ase_sf IPR005135, Endo/exonuclease/phosphatase |
PANTHERi | PTHR22748, PTHR22748, 1 hit |
Pfami | View protein in Pfam PF03372, Exo_endo_phos, 1 hit |
SUPFAMi | SSF56219, SSF56219, 1 hit |
TIGRFAMsi | TIGR00633, xth, 1 hit |
PROSITEi | View protein in PROSITE PS00726, AP_NUCLEASE_F1_1, 1 hit PS00728, AP_NUCLEASE_F1_3, 1 hit PS51435, AP_NUCLEASE_F1_4, 1 hit |
(1+)i Sequence
Sequence statusi: Complete.
This entry has 1 described isoform and 8 potential isoforms that are computationally mapped.Show allAlign All
A0MTA1-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG
60 70 80 90 100
RAANMKITSW NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD
110 120 130 140 150
ITGMPEYPHK YWAGSEDKEG YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV
160 170 180 190 200
ITAEFPDFFL VTAYVPNASR GLVRLDYRKT WDVDFRAYLC GLDARKPLVL
210 220 230 240 250
CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG FTDSFRELYP
260 270 280 290 300
DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD
310
HCPITLFLAV
Computationally mapped potential isoform sequencesi
There are 8 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketF1QTR9 | F1QTR9_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 341 | Annotation score: | ||
A0A0R4IWF9 | A0A0R4IWF9_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 340 | Annotation score: | ||
H0WEZ7 | H0WEZ7_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 220 | Annotation score: | ||
A0A2R9YJQ0 | A0A2R9YJQ0_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 310 | Annotation score: | ||
H0WED1 | H0WED1_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 189 | Annotation score: | ||
H0WFG1 | H0WFG1_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 116 | Annotation score: | ||
H0WFB7 | H0WFB7_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 170 | Annotation score: | ||
H0WEW8 | H0WEW8_DANRE | DNA-(apurinic or apyrimidinic site)... | apex1 | 105 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 16 | A → S in CAI11781 (PubMed:23594743).Curated | 1 | |
Sequence conflicti | 80 – 93 | Missing in AAI64240 (Ref. 3) CuratedAdd BLAST | 14 | |
Sequence conflicti | 80 – 93 | Missing in AAH97053 (Ref. 3) CuratedAdd BLAST | 14 | |
Sequence conflicti | 103 | G → A in AAH55545 (Ref. 3) Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | EF041101 mRNA Translation: ABK35081.1 EF041102 mRNA Translation: ABK35082.1 EF041103 Genomic DNA Translation: ABK35083.1 EF041104 Genomic DNA Translation: ABK35084.1 BX323558 Genomic DNA Translation: CAI11781.1 BC055545 mRNA Translation: AAH55545.1 BC097053 mRNA Translation: AAH97053.1 BC164240 mRNA Translation: AAI64240.1 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | EF041101 mRNA Translation: ABK35081.1 EF041102 mRNA Translation: ABK35082.1 EF041103 Genomic DNA Translation: ABK35083.1 EF041104 Genomic DNA Translation: ABK35084.1 BX323558 Genomic DNA Translation: CAI11781.1 BC055545 mRNA Translation: AAH55545.1 BC097053 mRNA Translation: AAH97053.1 BC164240 mRNA Translation: AAI64240.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2O3C | X-ray | 2.30 | A/B/C | 33-310 | [»] | |
SMRi | A0MTA1 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 7955.ENSDARP00000067373 |
Proteomic databases
PaxDbi | A0MTA1 |
PeptideAtlasi | A0MTA1 |
PRIDEi | A0MTA1 |
Organism-specific databases
ZFINi | ZDB-GENE-040426-2761, apex1 |
Phylogenomic databases
eggNOGi | KOG1294, Eukaryota |
InParanoidi | A0MTA1 |
PhylomeDBi | A0MTA1 |
TreeFami | TF315048 |
Enzyme and pathway databases
Reactomei | R-DRE-110357, Displacement of DNA glycosylase by APEX1 R-DRE-110362, POLB-Dependent Long Patch Base Excision Repair R-DRE-110373, Resolution of AP sites via the multiple-nucleotide patch replacement pathway R-DRE-5651801, PCNA-Dependent Long Patch Base Excision Repair R-DRE-73930, Abasic sugar-phosphate removal via the single-nucleotide replacement pathway R-DRE-73933, Resolution of Abasic Sites (AP sites) |
Miscellaneous databases
EvolutionaryTracei | A0MTA1 |
PROi | PR:A0MTA1 |
Family and domain databases
Gene3Di | 3.60.10.10, 1 hit |
InterProi | View protein in InterPro IPR004808, AP_endonuc_1 IPR020847, AP_endonuclease_F1_BS IPR020848, AP_endonuclease_F1_CS IPR036691, Endo/exonu/phosph_ase_sf IPR005135, Endo/exonuclease/phosphatase |
PANTHERi | PTHR22748, PTHR22748, 1 hit |
Pfami | View protein in Pfam PF03372, Exo_endo_phos, 1 hit |
SUPFAMi | SSF56219, SSF56219, 1 hit |
TIGRFAMsi | TIGR00633, xth, 1 hit |
PROSITEi | View protein in PROSITE PS00726, AP_NUCLEASE_F1_1, 1 hit PS00728, AP_NUCLEASE_F1_3, 1 hit PS51435, AP_NUCLEASE_F1_4, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | APEX1_DANRE | |
Accessioni | A0MTA1Primary (citable) accession number: A0MTA1 Secondary accession number(s): Q4V955, Q5RHZ7, Q7SXL6 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | January 11, 2011 |
Last sequence update: | December 12, 2006 | |
Last modified: | December 2, 2020 | |
This is version 87 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families