Page last updated: 2024-10-24

DNA-(apurinic or apyrimidinic site) endonuclease activity

Definition

Target type: molecularfunction

Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER). [Wikipedia:AP_endonuclease]

DNA-(apurinic or apyrimidinic site) endonuclease activity, also known as AP endonuclease activity, is a critical function in DNA repair pathways. This activity is catalyzed by enzymes called AP endonucleases, which specifically recognize and cleave the phosphodiester backbone of DNA at abasic sites, also known as apurinic/apyrimidinic (AP) sites. These sites arise from spontaneous hydrolytic depurination or depyrimidination events, where a purine or pyrimidine base is lost from the DNA strand.

AP endonucleases play a key role in the base excision repair (BER) pathway, one of the major mechanisms for repairing damaged or modified DNA bases. The BER pathway involves the following steps:

1. **Recognition and Cleavage**: The AP endonuclease recognizes the AP site and cleaves the phosphodiester bond 5' to the abasic site, creating a 5' phosphate and a 3' hydroxyl group. This cleavage step generates a single-stranded DNA break, which facilitates further repair.

2. **Removal of AP Site**: Following cleavage, the 5' deoxyribose phosphate (dRP) residue, which remains attached to the 5' phosphate, is removed by a separate enzyme called dRP lyase.

3. **Gap Filling and Ligation**: The resulting single-stranded gap is then filled in by DNA polymerase, using the undamaged complementary strand as a template. Finally, the nick is sealed by DNA ligase.

By removing damaged or modified bases and restoring the integrity of the DNA sequence, AP endonuclease activity safeguards the genome from mutations and other harmful consequences. This activity is essential for maintaining the stability and functionality of the genetic code, ensuring the proper expression of genes and the accurate transmission of genetic information.
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Proteins (8)

ProteinDefinitionTaxonomy
Formamidopyrimidine-DNA glycosylaseA formamidopyrimidine-DNA glycosylase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P05523]Escherichia coli K-12
Endonuclease 8-like 1An endonuclease 8-like 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96FI4]Homo sapiens (human)
DNA polymerase betaA DNA polymerase beta that is encoded in the genome of human. [PRO:CNA]Homo sapiens (human)
Endonuclease 8-like 1An endonuclease 8-like 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96FI4]Homo sapiens (human)
Endonuclease III-like protein 1An endonuclease III-like protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P78549]Homo sapiens (human)
DNA-(apurinic or apyrimidinic site) endonucleaseA DNA-(apurinic or apyrimidinic site) endonuclease that is encoded in the genome of human. [PRO:DNx, UniProtKB:P27695]Homo sapiens (human)
40S ribosomal protein S3A eukaryotic-type small ribosomal subunit protein uS3 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P23396]Homo sapiens (human)
DNA polymerase betaA DNA polymerase beta that is encoded in the genome of human. [PRO:CNA]Homo sapiens (human)

Compounds (42)

CompoundDefinitionClassesRoles
digallic aciddigallic acid: structure given in first sourcebenzoate ester;
gallate ester
aurintricarboxylic acidaurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'.

Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues.
monohydroxybenzoic acid;
quinomethanes;
tricarboxylic acid
fluorochrome;
histological dye;
insulin-like growth factor receptor 1 antagonist
hycanthonehycanthone : A thioxanthen-9-one compound having a hydroxymethyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. It was formerly used (particularly as the monomethanesulfonic acid salt) as a schistosomicide for individual or mass treatement of infection with Schistosoma haematobium and S. mansoni, but due to its toxicity and concern about possible carcinogenicity, it has been replaced by other drugs such as praziquantel.

Hycanthone: Potentially toxic, but effective antischistosomal agent, it is a metabolite of LUCANTHONE.
thioxanthenesmutagen;
schistosomicide drug
isoniazidHydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals.

hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC).
carbohydrazideantitubercular agent;
drug allergen
pamoic acidpamoic acid: RN given refers to parent cpd; structuredicarboxylic acid
lucanthonelucanthone : A thioxanthen-9-one compound having a methyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. Formerly used for the treatment of schistosomiasis. It is a prodrug, being metabolised to hycanthone.

Lucanthone: One of the SCHISTOSOMICIDES, it has been replaced largely by HYCANTHONE and more recently PRAZIQUANTEL. (From Martindale The Extrapharmacopoeia, 30th ed., p46)
thioxanthenesadjuvant;
antineoplastic agent;
EC 5.99.1.2 (DNA topoisomerase) inhibitor;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
mutagen;
photosensitizing agent;
prodrug;
schistosomicide drug
Dillapiole5-allyl 6,7-dimethoxy 1,3-benzodioxole: a plant based insecticide; structure in first sourcebenzodioxolesmetabolite
oleanolic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
plant metabolite
zidovudinezidovudine : A pyrimidine 2',3'-dideoxyribonucleoside compound having a 3'-azido substituent and thymine as the nucleobase.

Zidovudine: A dideoxynucleoside compound in which the 3'-hydroxy group on the sugar moiety has been replaced by an azido group. This modification prevents the formation of phosphodiester linkages which are needed for the completion of nucleic acid chains. The compound is a potent inhibitor of HIV replication, acting as a chain-terminator of viral DNA during reverse transcription. It improves immunologic function, partially reverses the HIV-induced neurological dysfunction, and improves certain other clinical abnormalities associated with AIDS. Its principal toxic effect is dose-dependent suppression of bone marrow, resulting in anemia and leukopenia.
azide;
pyrimidine 2',3'-dideoxyribonucleoside
antimetabolite;
antiviral drug;
HIV-1 reverse transcriptase inhibitor
mitoxantrone hydrochloridehydrochlorideantineoplastic agent
ursolic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
geroprotector;
plant metabolite
thymidine 5'-triphosphatedTTP : A thymidine phosphate having a triphosphate group at the 5'-position.

thymidine 5'-triphosphate: RN given refers to parent cpd
pyrimidine 2'-deoxyribonucleoside 5'-triphosphate;
thymidine phosphate
Escherichia coli metabolite;
mouse metabolite
betulinic acidhydroxy monocarboxylic acid;
pentacyclic triterpenoid
anti-HIV agent;
anti-inflammatory agent;
antimalarial;
antineoplastic agent;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
plant metabolite
calanolide a(+)-calanolide A : An organic heterotetracyclic compound that is 11,12-dihydro-2H,6H,10H-dipyrano[2,3-f:2',3'-h]chromen-2-one substituted by a hydroxy group at position 12, methyl groups at positions 6, 6, 10 and 11 and a propyl group at position 4 (the 10R,11S,12S stereoisomer). Isolated from Calophyllum lanigerum var austrocoriaceum and Calophyllum brasiliense, it exhibits potent activity against HIV-1 reverse transcriptase.

calanolide A: NSC 661122 and costatolide are isomers; a novel HIV-inhibitory class of coumarin derivatives from the tropical rainforest tree, Calophyllum lanigerum (Clusiaceae); structure in first source
cyclic ether;
delta-lactone;
organic heterotetracyclic compound;
secondary alcohol
HIV-1 reverse transcriptase inhibitor;
plant metabolite
2',3'-dideoxythymidine triphosphateddTTP : A pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate having thymine as the nucleobase.pyrimidine 2',3'-dideoxyribonucleoside 5'-triphosphate;
thymidine phosphate
2',3'-dideoxyadenosine triphosphatepurine deoxyribonucleoside triphosphate
zidovudine triphosphate
illimaquinoneillimaquinone: structure given in first source; isolated from the Red Sea sponge Smenospongia; inhibits the RNase H. activity of HIV-1 reverse transcriptasemonohydroxy-1,4-benzoquinones;
prenylquinone
metabolite
7-nitro-1h-indole-2-carboxylic acid7-nitro-1H-indole-2-carboxylic acid: acts on AP endonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities of APE1; structure in first source
3,3',4,4',5,5'-hexabromobiphenyl
6-hydroxydopa6-hydroxydopa: RN given refers to cpd without isomeric designationnon-proteinogenic alpha-amino acid
tanshinone ii atashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first sourceabietane diterpenoid
sitosterol, (3beta)-isomersitosterol : A member of the class of phytosterols that is stigmast-5-ene substituted by a beta-hydroxy group at position 3.

Sobatum: tradename; active fraction of Solanum trilobatum; reduces side-effects of radiation-induced toxicity
3beta-hydroxy-Delta(5)-steroid;
3beta-sterol;
C29-steroid;
phytosterols;
stigmastane sterol
anticholesteremic drug;
antioxidant;
mouse metabolite;
plant metabolite;
sterol methyltransferase inhibitor
TTPpyrimidine ribonucleoside 5'-triphosphate
aphidicolinaphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication.

Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells.
tetracyclic diterpenoidantimicrobial agent;
antimitotic;
antineoplastic agent;
antiviral drug;
apoptosis inducer;
Aspergillus metabolite;
DNA synthesis inhibitor;
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor;
fungal metabolite
1,3,6-trimethylpyrimido[5,4-e][1,2,4]triazine-5,7-dionepyrimidotriazine
2-[[5-(dimethylsulfamoyl)-1H-indol-3-yl]methylidene]propanedioic acid diethyl esterindoles
1,6-dimethyl-3-propylpyrimido[5,4-e][1,2,4]triazine-5,7-dionepyrimidotriazine
stigmasterolstigmasta-5,22-dien-3-ol: isolated from freeze-dried powder of Blackberries (Rubus ursinus L.) which showed an activity on inhibition of chemocarcinogen

stigmasterol : A 3beta-sterol that consists of 3beta-hydroxystigmastane having double bonds at the 5,6- and 22,23-positions.
3beta-hydroxy-Delta(5)-steroid;
3beta-sterol;
phytosterols;
stigmastane sterol
plant metabolite
myricetin7-hydroxyflavonol;
hexahydroxyflavone
antineoplastic agent;
antioxidant;
cyclooxygenase 1 inhibitor;
food component;
geroprotector;
hypoglycemic agent;
plant metabolite
ag 538AG 538: an IGF-1 receptor kinase inhibitor; structure in first source
lyonisidedaucosterol : A steroid saponin that is sitosterol attached to a beta-D-glucopyranosyl residue at position 3 via a glycosidic linkage. It has bee isolated from Panax japonicus var. major and Breynia fruticosa.beta-D-glucoside;
monosaccharide derivative;
steroid saponin
plant metabolite
e 3330E 3330: structure given in first source; MW 378.47
corosolic acidtriterpenoidmetabolite
gentamicin sulfate
edgeworinedgeworin: from Dirca occidentalis Gray; structure given in first source
N-[3-(1,3-benzothiazol-2-yl)-5,6-dihydro-4H-thieno[2,3-c]pyrrol-2-yl]acetamidebenzothiazoles
raltegravir1,2,4-oxadiazole;
dicarboxylic acid amide;
hydroxypyrimidine;
monofluorobenzenes;
pyrimidone;
secondary carboxamide
antiviral drug;
HIV-1 integrase inhibitor
GS-443902GS-441524 triphosphate: intracellular active metabolite of remdesivir

GS-443902 : An organic triphosphate that is GS-441524 in which the 5'-hydroxy group has been replaced by a triphosphate group. It is the active metabolite of remdesivir.
aromatic amine;
C-nucleoside;
nitrile;
organic triphosphate;
pyrrolotriazine
anticoronaviral agent;
antiviral drug;
drug metabolite
PF-06446846PF-06446846 : A triazolopyridine that is 3H-[1,2,3]triazolo[4,5-b]pyridine substituted by a 4-{(3-chloropyridin-2-yl)[(3R)-piperidin-3-yl]carbamoyl}phenyl group at position 3. It is a potent inhibitor of PCSK9.

PF-06446846: inhibits translation of PCSK9 ;structure in first source
benzamides;
monochloropyridine;
piperidines;
tertiary carboxamide;
triazolopyridine
antilipemic drug;
EC 3.4.21.61 (kexin) inhibitor
thiolactomycinthiolactomycin: from actinomycetes; structure given in first source
galloflavingalloflavin: structure in first source