Information on EC 4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase and Organism(s) Homo sapiens

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The enzyme appears in selected viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.2.99.18
-
RECOMMENDED NAME
GeneOntology No.
DNA-(apurinic or apyrimidinic site) lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
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
show the reaction diagram
mechanism
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
beta-elimination
-
-
endonuclease activity
-
-
endonuclease reaction
hydrolysis
-
-
phospho-group transfer
-
-
additional information
-
APE1 possesses endonuclease, exonuclease and phosphodiesterase activity
SYSTEMATIC NAME
IUBMB Comments
DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase
'Nicking' of the phosphodiester bond is due to a lyase-type reaction, not hydrolysis. This group of enzymes was previously listed as endonucleases, under EC 3.1.25.2.
CAS REGISTRY NUMBER
COMMENTARY hide
60184-90-9
-
61811-29-8
-
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(pT)7(p(2,3-dihydroxy-5-oxopentyl phosphate))(pT)6
?
show the reaction diagram
-
-
-
-
?
12-mer oligodeoxyribonucleotide containing a 2'-deoxyguanosine at the natural AP site
?
show the reaction diagram
-
-
-
-
-
12-mer oligodeoxyribonucleotide containing a natural AP site
?
show the reaction diagram
-
the minimal kinetic model for the natural AP site incision consists of four stages corresponding to three different transient states of APE1. When the enzyme is complexed with the AP-substrate, the catalytic cycle is completed within 3 s
-
-
?
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
?
show the reaction diagram
-
-
-
-
-
34FDNA
?
show the reaction diagram
-
-
-
-
?
34FRNA
?
show the reaction diagram
-
-
-
-
?
43-mer oligonucleotide containing apurinic/apyrimidinic sites
fragments of DNA
show the reaction diagram
-
-
-
-
?
43-mer oligonucleotide containing the AP-site analog tetrahydrofuran at nt 31
?
show the reaction diagram
-
-
-
-
?
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
?
show the reaction diagram
-
the fluorogenic substrate OligoI is based on the sequence immediately surrounding the stem V-loop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide
-
-
?
5'-Cy3-CAAGGTAGTTATCCTTG-1-Black Hole Quencher1-3'
?
show the reaction diagram
-
the fluorogenic substrate DNAOligoI is based on the sequence immediately surrounding the stem Vloop region (OligoI) and incorporating a fluorescent tag, Cy3, at the 5' end and a fluorescence Black Hole Quencher at the 3' end of the oligonucleotide, DNAOligoI has an identical sequence to OligoI except that deoxythymidylate is substituted for 2' hydroxyl uridine
-
-
?
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
?
show the reaction diagram
-
a synthetic stable AP-site analog where X represents tetrahydrofuran
-
-
?
AP-DNA
fragments of DNA
show the reaction diagram
Base excision repair pathway, enzyme cleaves the 5'-phosphodiester bond, generating 3'-OH and 5'-dRP termini
-
-
?
AP-DNA-DNA
?
show the reaction diagram
-
synthetic DNA-DNA hybrid
-
-
?
AP-DNA-RNA
?
show the reaction diagram
-
synthetic DNA-RNA hybrids that simulate a transcription intermediate
-
-
?
c-myc coding region determinant mRNA
?
show the reaction diagram
-
APE1 preferentially cleaves in between UA and CA dinucleotides of c-myc coding region determinant RNA
-
-
?
c-myc RNA
?
show the reaction diagram
-
APE1 cleaves at the UA, CA, and UG sites of c-myc RNA in vitro
-
-
?
CAAXACCTTCATCCTTTCC
?
show the reaction diagram
-
X: AP site
-
-
?
CAXAACCTTCATCCTTTCC
?
show the reaction diagram
-
X: AP site
-
-
?
CTAGTCAXCACTGTCTGTGGATAC
?
show the reaction diagram
-
X: AP site
-
-
?
CXAAACCTTCATCCTTTCC
?
show the reaction diagram
-
X: AP site
-
-
?
DNA
fragments of DNA
show the reaction diagram
DNA containing 5-OH-C/A
?
show the reaction diagram
-
-
-
-
-
DNA containing 5-OH-C/G
?
show the reaction diagram
-
-
-
-
-
DNA containing an abasic site
?
show the reaction diagram
-
45-mer oligomer
-
-
?
DNA containing apurinic/apyrimidinic site
DNA fragments
show the reaction diagram
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
show the reaction diagram
-
hydrogen bonds to phosphate groups 3' to the cleavage site is essential for the binding of the enzyme to the product DNA, which may be necessary for efficient functioning of the base excision rapair pathway
-
-
?
DNA containing dihydrouracil
?
show the reaction diagram
-
-
-
-
-
DNA containing tamdem dihydrouracil
?
show the reaction diagram
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA containing tandem dihydrouracil
?
show the reaction diagram
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA with 2-deoxyribonolactone
?
show the reaction diagram
-
-
-
-
-
double-stranded DNA with abasic sites
?
show the reaction diagram
-
-
-
-
?
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
?
show the reaction diagram
-
nucleotide incison repair activity
-
-
?
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
?
show the reaction diagram
-
nucleotide incison repair activity
-
-
?
duplex oligonucleotide containing a tetrahydrofuran*G pair
?
show the reaction diagram
-
nucleotide incison repair activity
-
-
?
GTACGTAXCCACAGACAGTGATGA
?
show the reaction diagram
-
X: AP site
-
-
?
oligodeoxynucleotide with abasic site 2,3-dihydroxy-5-oxopentyl phosphate
?
show the reaction diagram
-
-
-
-
?
oligomer with G/U pair
?
show the reaction diagram
-
-
-
-
-
Red substrate 2
?
show the reaction diagram
-
-
-
-
?
single-stranded DNA with abasic sites
?
show the reaction diagram
-
catalytic efficiency is 20fold less than the activity against double-stranded DNA with abasic sites
-
-
?
THF-containing oligonucleotide
?
show the reaction diagram
-
AP endonuclease activity
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
AP-DNA
fragments of DNA
show the reaction diagram
P27695
Base excision repair pathway, enzyme cleaves the 5'-phosphodiester bond, generating 3'-OH and 5'-dRP termini
-
-
?
DNA
fragments of DNA
show the reaction diagram
DNA containing apurinic/apyrimidinic site
DNA fragments
show the reaction diagram
-
-
-
-
?
DNA containing apurinic/apyrimidinic sites
fragments of DNA
show the reaction diagram
-
hydrogen bonds to phosphate groups 3' to the cleavage site is essential for the binding of the enzyme to the product DNA, which may be necessary for efficient functioning of the base excision rapair pathway
-
-
?
DNA containing tamdem dihydrouracil
?
show the reaction diagram
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
DNA containing tandem dihydrouracil
?
show the reaction diagram
-
the human AP endonuclease APE1 can process the 3' termini generated by human endonuclease III (hNTH) and endonuclease VIII. Both human endonuclease III and endonuclease VIII cannot completely remove both dihydrouracil lesions. With the participation of APE1 and polynucleotide kinase, the 3'-lesions remaining in the products of the reaction with human endonuclease III and endonuclease VIII can efficiently removed. The resulting products can be utilized by repair DNA polymerases as primers for repair synthesis
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
CoCl2 (500 microM) is essential for AP endonuclease assay. Effects of Co on APE/Ref-1 are concentration dependent
Fe
-
pro-inflammatory activity of iron in the lung injury, at least in part, because of its induction of APE/Ref-1
Fe2+
-
Fe2+ is able to support the incision activity of the enzyme at excess protein to DNA ratios of at least 6:1, Mg2+ and Fe2+ compete for the same metal-binding site
Iron
[4Fe-4S]-cluster; iron-sulfur protein
MgCl2
-
tetrahydrofuran*G incision is efficiently catalyzed at 0.001 mM Mg2+, 5 mM MgCl2 are required for optimal AP endonuclease activity
Na+
-
65 mM included in assay medium
Sm2+
-
the divalent metal ion soaked with the protein crystals is found specifically to associate with the glutamate residue
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(pA)10
-
-
(pA)10*d(pT)10
-
-
-
(pA)11*d(pT)11
-
-
-
(pA)12
-
-
-
(pA)16
-
-
-
(pA)16*d(pT)16
-
-
-
(pA)2
-
-
(pA)3
-
-
(pA)4
-
-
(pA)4*d(pT)4
-
-
-
(pA)6
-
-
(pA)6*d(pT)6
-
-
-
(pA)8
-
-
(pA)8*d(pT)8
-
-
-
(pA)9
-
-
(pC)10
-
-
(pC)14
-
-
-
(pC)2
-
-
(pC)4
-
-
(pC)6
-
-
(pC)8
-
-
(pU)10
-
-
(pU)10*(pA)10
-
-
-
(pU)11
-
-
-
(pU)16
-
-
-
(pU)16*(pA)16
-
-
-
(pU)4
-
-
(pU)4*(pA)4
-
-
-
(pU)6
-
-
(pU)6*(pA)6
-
-
-
(pU)8
-
-
(pU)9
-
-
(pU)9*(pA)9
-
-
-
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
-
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
2,2'-(2-oxo-1H-benzimidazole-1,3(2H)-diyl)diacetic acid
-
-
2,2'-(3,7-dioxo-5,7-dihydro-1H,3H-benzo[1,2-c:4,5-c']difuran-1,5-diyl)diacetic acid
-
-
2,2'-[(2,5-dimethylfuran-3,4-diyl)bis(carbonylimino)]diacetic acid
-
-
2,2'-[(6-oxo-6H-benzo[c]chromene-1,3-diyl)bis(oxy)]dipropanoic acid
-
-
2,2'-[(6-phenylpyrimidine-2,4-diyl)disulfanediyl]diacetic acid
-
-
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
-
-
2,4,9-trimethylbenzo[b][1,8]naphthyridin-5-amine
-
i.e. Ape1 repair inhibitor 03, specific inhibitor of AP endonuclease
2-((Z)-2-oxo-3-(4-oxo-2-thioxothiazolidin-5-ylidene)indolin-1-yl)acetic acid
-
potent inhibitory activity
2-(4-(2,5-dimethyl-1H-prryol-1-yl)phenoxy) acetic acid
-
i.e. Ape1 repair inhibitor 01, specific inhibitor of AP endonuclease
2-(5-((2-(2-carboxyphenyl)-1,3-dioxo)-2,3-dihydro-1H-isoindol-5-yl)carbonyl}-1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)benzoic acid
-
potent inhibitory activity
2-mercaptoethanol
suppresses delta-elimination partially
2-[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
-
-
3,3'-(1,3,4-thiadiazole-2,5-diyldisulfanediyl)dipropanoic acid
-
-
3,3'-(2-thioxo-1H-benzimidazole-1,3(2H)-diyl)dipropanoic acid
-
-
3-((3,4-dimethylphenoxy)methyl)furan-2-carboxylic acid
-
-
3-((pyridin-2-ylthio)methyl)benzofuran-2-carboxylic acid
-
-
3-(1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl)propanoic acid
-
potent inhibitory activity
3-(1-(carboxymethyl)-5-(4-fluorophenyl)-1H-pyrrol-2-yl)propanoic acid
-
potent inhibitory activity
3-(1-(carboxymethyl)-5-(thiophen-2-yl)-1H-pyrrol-2-yl)propanoic acid
-
potent inhibitory activity
3-(1-(carboxymethyl)-5-p-tolyl-1H-pyrrol-2-yl)propanoic acid
-
-
3-(2-carboxyethyl)-4-hydroxyquinoline-6-carboxylic acid
-
-
3-(5-((E)-(3-(carboxymethyl)-4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl)furan-2-yl)benzoic acid
-
potent inhibitory activity
3-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]propanoic acid
-
-
3-[(6-amino-9H-purin-8-yl)sulfanyl]propanoic acid
-
-
3-[5-(2,3-dimethoxy-6-methyl-1,4-benzoquinoyl)]-2-nonyl-2-propionic acid
E3330 specifically blocking the APE1 redox but not DNA activity, an equilibrium constant (KD) of 1.6 nM is obtained for the binding of E3330 to APE1. E3330 is also shown to block the ability of APE1 to reduce NF-kappaB, thus interfering with the redox activity of APE1
3-[[4-(carboxymethyl)benzyl]sulfanyl]-8-methyl-5H-[1,2,4]triazino[5,6-b]indole-5-carboxylic acid
-
-
4-((2-carboxyphenoxy)methyl)-2,5-dimethylfuran-3-carboxylic acid
-
potent inhibitory activity
4-(2,6,8-trimethylquinolin-4-ylamino)phenol
-
i.e. Ape1 repair inhibitor 02, specific inhibitor of AP endonuclease
4-(4-(4-carboxyphenoxy)phenylsulfonyl)benzene-1,2-dioic acid
-
-
4-(4-(4-carboxyphenylsulfonyl)phenyl)sulfanylbenzene-1,2-dioic acid
-
potent inhibitory activity
4-(4-(4-carboxyphenylthio)phenylsulfonyl)benzene-1,2-dioic acid
-
potent inhibitory activity
4-([[(3-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-5-methylfuran-2-carboxylic acid
-
-
4-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]butanoic acid
-
-
4-[[(2-carboxypropyl)sulfanyl]methyl]-5-methylfuran-2-carboxylic acid
-
-
5,5'-[methanediylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
-
-
5-(((tetrahydrofuran-2-yl)methylthio)methyl)-2-methylfuran-3-carboxylic acid
-
-
5-([[(4-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-3-methylfuran-2-carboxylic acid
-
-
6-hydroxy-DL-DOPA
-
complete inhibition at 0.1 mM
7-nitro-1H-indole 2-carboxylic acid
-
CRT0044876, binds to the active site of APE/Ref-1 and effectively inhibits its AP endonuclease, 3'-phosphodiesterase and 3'-phosphatase activities at low micromolar concentrations
7-nitro-1H-indole-2-carboxylic acid
-
CRT0044876
8-[(2E)-2-(3-methoxybenzylidene)hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
inhibitor induces time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with its potency to inhibit APE-1 endonuclease excision. The inhibitor also potentiates by 5fold the toxicity of a DNA methylating agent that creates abasic sites
A1NI2-A3NI1
-
-
ATP
-
in presence of 1 mM Mg2+, Ape1 incision activity is inhibited at higher ATP concentrations (2-5 mM). Depending on the relative concentration of Mg2+, ATP can have both inhibitory and stimulatory consequences on Ape1 incision capacity
aurintricarboxylic acid
-
potent inhibitor of APE1
Ca2+
-
50% inhibition at 5-10 mM
ceftriaxone sodium
-
-
cephapirin sodium
-
-
d(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))
-
-
d(p(2,3-dihydroxy-5-oxopentyl phosphate))
-
-
d(pA)10
-
-
d(pA)10*d(pT)10
-
-
-
d(pA)12
-
-
d(pA)12*d(pT)12
-
-
-
d(pA)14
-
-
d(pA)14*d(pT)14
-
-
-
d(pA)16
-
-
d(pA)16*d(pT)16
-
-
-
d(pA)2
-
-
d(pA)2*d(pT)2
-
-
-
d(pA)20*(pT)20
-
-
-
d(pA)4
-
-
d(pA)4*d(pT)4
-
-
-
d(pA)6
-
-
d(pA)6*d(pT)6
-
-
-
d(pA)8
-
-
d(pA)8*d(pT)8
-
-
-
d(pC)10
-
-
d(pC)11
-
-
-
d(pC)13
-
-
-
d(pC)2
-
-
d(pC)3
-
-
d(pC)5
-
-
d(pC)7
-
-
d(pC)9
-
-
d(pG)2
-
-
d(pG)4
-
-
d(pG)6
-
-
d(pG)8
-
-
d(pT)10
-
-
d(pT)11
-
-
-
d(pT)12
-
-
-
d(pT)14
-
-
-
d(pT)15
-
-
-
d(pT)2
-
-
d(pT)3
-
-
d(pT)4
-
-
d(pT)6
-
-
d(pT)8
-
-
dAMP
-
-
dCMP
-
-
dGMP
-
-
dTMP
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))3pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))5pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))7pT]
-
-
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))9pT]
-
-
E3330
Fe2+
-
inhibitory effects on APE/Ref-1 activity
Harmane
-
i.e. 1-methyl-9H-pyrido-[3,4-b]indole, only slight inhibition of AP endocunlease I and II
isoflavones
-
soy isoflavones decrease apurinic/apyrimidinic endonuclease 1/redox factor-1 expression
K+
-
K+ is inhibitory to the native APE1 at 0.2-10 mM with approximately 5fold inhibition
lucanthone
-
inhibits repair activity from cellular extracts and enhances cell killing effect of the laboratory alkylating agent methyl methanesulfonate and the clinically relevant agent temozolomide, no inhibition of redox function or exonuclease activity on mismatched nucleotides
MgCl2
-
tetrahydrofuran*G incision activity is inhibited above 2 mM
Mitoxantrone
-
-
Mn2+
-
50% inhibition at 5-10 mM
myricetin
-
above 80% inhibition at 0.1 mM
N-(3-chlorophenyl)-5,6-dihyro-4H-cyclopenta[d]isoxazole-3-carboxamide
-
i.e. Ape1 repair inhibitor 06, specific inhibitor of AP endonuclease
N-ethylmaleimide
NaH2PO4
-
-
NSC-13755
-
complete inhibition at 0.1 mM
P53
-
after camptothecin treatment, p53 is a negative regulator of APE1 expression, APE1 promoter activity is repressed by wild-type p53, but not by mutant p53
Pb2+
-
inhibitory effects on APE/Ref-1 activity
PNRI-299
-
inhibition on AP-1 transcription
polyinosinic-polycytidylic acid
-
transfection of APE1 suppresses the extracellular release of high-mobility group box 1 in response to polyinosinic-polycytidylic acid stimulation
-
proteinBcl2
-
overexpression of Bcl2, a major cellular oncogenic protein, in cells reduces formation of the APE1-XRCC1 complex, Bcl2 not only prolongs cell survival but also suppresses the repair of abasic (AP) sites of DNA lesions. Bcl2 directly interacts with APE1 via its BH domains, and deletion of any of the BH domains from Bcl2 results in loss of the ability of Bcl2 to suppress APE1 endonuclease activity and AP site repair
-
Reactive blue 2
-
above 80% inhibition at 0.1 mM
reactive oxygen species
-
reactive oxygen species not only can inhibit APE/Ref-1 activities by direct oxidation of amino acid residues, but also affects the expression level and subcellular localization of APE/Ref-1
-
resveratrol
-
dock into one of the two drug-treatable pockets located in the redox domain
RPA proteins
RPA proteins are able to suppress the APE1 endonuclease activity in ssDNA of a replicative fork but not in a transcription bubble or in dsDNA
-
tyrphostin AG 538
-
mild inhibition at 0.1 mM
[(3Z)-3-(3-[[(2-hydroxyphenyl)carbonyl]amino]-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
-
-
[(3Z)-3-[3-(4-bromophenyl)-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene]-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
-
-
[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
-
-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8-oxoguanine-DNA glycosylase
-
OGG1 stimulates the hydrolytic activity of AP endonuclease
-
APE1
-
APE1, a human homolog of Escherichia coli exonuclease III Xth stimulates under conditions of Vmax
-
ATP
-
in presence of 1 mM Mg2+, Ape1 abasic endonuclease activity is stimulated (1.75- and 1.25-fold at 0.5 and 1 mM ATP concentrations). At 10 mM MgCl2, the higher concentrations of ATP has stimulatory effects on AP site incision by Ape1
cisplatin
-
2fold increase in Y-box-binding protein-1/hNTH1 complex formation in transfected MCF-7 cells after a treatment of 12 microM cisplatin for 4 h
cockayne syndrome B protein
-
DNA-dependent ATPase CSB
-
in presence of 1 mM Mg2+, enzyme stimulates AP site incision by Ape1 in the absence of ATP on both fully paired duplex DNA (42F-42Comp) and an 11-nt bubble duplex substrate containing a centrally located abasic site (42F-42bubbleComp). When 2.5 mM ATP is included in the reactions with 1 mM MgCl2, inhibition of Ape1 incision activity is detected
-
Helicobacter pylori (CagA+) water-extract protein (HPWEP)
-
HPWEP-stimulation significantly increases APE-1 mRNA expression levels in human peripheral macrophages. HPWEP-stimulation increases APE-1 expression levels in AGS cells. HPWEP stimulation increases APE-1 protein expression in gastric epithelial MKN-28 cells in a dose-dependent manner (1:30 and 1:10 dilution). When normalized to beta-actin, HPWEP stimulation at a 1:10 dilution significantly increases APE-1 protein expression compared to control MKN-28 cells. APE-1 protein expression is further increased in HPWEP (1:10 dilution) stimulated MKN-28 cells after treatment with hypo/reoxygenation.
-
imidazole
-
enhances activity of wild-type enzyme markedly, enhances Y171A somewhat and fails to enhance Y171F. When stoichiometric levels of tyrosine are included in the reaction with imidazole, wild-type enzyme as well as mutant enzymes are stimulated. Degree of stimulation of wild-type enzyme continues to exceed that of the mutants
lipopolysaccharide
-
100 ng/ml lipopolysaccharide stimulates the upregulation and nuclear translocation of APE1 in activated macrophages. APE1 critically mediates both the translocation of NF-B to the nucleus and the expression of inducible nitric oxide synthase by murine macrophage RAW264.7 cells after stimulation with LPS
UV light
-
3fold increase in Y-box-binding protein-1/hNTH1 complex formation in transfected MCF-7 cells after a treatment with a UV irradiation dose of 40 J/m2 tested for 4 h
-
Y-box-binding protein-1
-
protein strongly stimulates in vitro the activity of hNTH1 toward DNA duplex probes containing oxidized bases, lesions prone to be present in cisplatin treated cells
-
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000093 - 0.00022
12-mer oligodeoxyribonucleotide containing a natural AP site
-
0.000098
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
-
wild-type, pH 7.5, 25C
-
0.000098
2-deoxyribonolactone
-
pH 7.6, room temperature
0.0001792
34FDNA
-
-
-
0.001561
34FRNA
-
-
-
0.0000034 - 0.0000278
43-mer oligonucleotide containing apurinic/apyrimidinic sites
-
0.0000368 - 0.0000536
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
0.000424
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
recombinant enzyme
-
0.00082
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
-
pH 7.5, 37C
-
0.0000238
AP-DNA-DNA
-
1 mM Mg2+
-
0.0000057
AP-DNA-RNA
-
1 mM Mg2+
-
0.0000213
apruinic/apyrimidinic site
-
pH 7.6, room temperature
-
0.000075 - 0.00062
apurinic site
-
dsDNA, pH 7.5, 37C
-
0.008
apurinic sites of DNA
-
-
-
0.0061
CAAXACCTTCATCCTTTCC
-
ssDNA, X: AP site, pH 7.5, 37C
-
0.0075
CAXAACCTTCATCCTTTCC
-
ssDNA, X: AP site, pH 7.5, 37C
-
0.013
CTAGTCAXCACTGTCTGTGGATAC
-
ssDNA, X: AP site, pH 7.5, 37C
-
0.0091
CXAAACCTTCATCCTTTCC
-
ssDNA, X = AP site, pH 7.5, 37C
-
0.001587 - 0.001689
DNA
0.00000007 - 0.0000035
DNA containing 5-OH-C/A
-
0.000000048 - 0.0000012
DNA containing 5-OH-C/G
-
100 - 413
DNA containing an abasic site
0.000069 - 0.00017
DNA containing dihydrouracil
-
0.000024
double-stranded DNA with abasic sites
-
-
-
0.0000084
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
-
pH 6.8, 37C, nucleotide incison repair activity
-
0.0000072
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
-
pH 6.8, 37C, nucleotide incison repair activity
-
0.0000027
duplex oligonucleotide containing a tetrahydrofuran*G pair
-
pH 6.8, 37C, nucleotide incison repair activity
-
0.0163
GTACGTAXCCACAGACAGTGATGA
-
ssDNA, X: AP site, pH 7.5, 37C
-
0.00005 - 0.0013
oligomer with G/U pair
-
0.065
Red substrate 2
-
-
-
0.000428
single-stranded DNA with abasic sites
-
-
-
0.000136 - 0.000154
THF-containing oligonucleotide
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000153 - 2.8
12-mer oligodeoxyribonucleotide containing a natural AP site
-
1
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
-
wild-type, pH 7.5, 25C
-
2.3
2-deoxyribonolactone
-
pH 7.6, room temperature
26500
34FDNA
-
-
-
438
34FRNA
-
-
-
2.91 - 3.36
43-mer oligonucleotide containing the AP-site analog THF at nt 31
-
0.0272
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
recombinant enzyme
-
3.2
5'-TCGAGGATCCTGAGCTCGAGTCGACGXTCGCGAATTCTGCGGATCCAAGC-3'
-
pH 7.5, 37C
-
174
AP-DNA-DNA
-
-
-
54
AP-DNA-RNA
-
-
-
2.4
apruinic/apyrimidinic site
-
pH 7.6, room temperature
-
10
apurinic/apyrimidinic site
-
5' cleavage of a reduced AP site
-
2340 - 16440
DNA
0.000035 - 0.0005
DNA containing 5-OH-C/A
-
0.000233 - 0.00117
DNA containing 5-OH-C/G
-
0.0007 - 10
DNA containing an abasic site
0.0000567 - 0.002
DNA containing dihydrouracil
-
4.1
double-stranded DNA with abasic sites
-
-
-
0.0027
duplex oligonucleotide containing a 5,6-dihydro-2'-deoxyuridine*G pair
-
pH 6.8, 37C, necleotide incison repair activity
-
0.002
duplex oligonucleotide containing a alpha-2'-deoxyadenosine*T pair
-
pH 6.8, 37C,nucleotide incison repair activity
-
0.002
duplex oligonucleotide containing a tetrahydrofuran*G pair
-
pH 6.8, 37C, nucleotide incison repair activity
-
0.0003 - 10
oligomer with G/U pair
-
4.2
single-stranded DNA with abasic sites
-
-
-
1020 - 12120
THF-containing oligonucleotide
-
additional information
additional information
-
wild-type APE1 cleaves AP sites more efficiently than D70A mutant with a kcat value for the incision of an AP site aproximately 10fold higher
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.63 - 30000
12-mer oligodeoxyribonucleotide containing a natural AP site
-
10000
12-mer oligodeoxyribonucleotide containing a tetrahydrofuran analogue at the natural AP site
-
wild-type, pH 7.5, 25C
-
64.15
5'-Cy3-CAAGGTAGTrUATCCTTG-1-Black Hole Quencher1-3'
-
recombinant enzyme
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.025
(p(2,3-dihydroxy-5-oxopentyl phosphate))
-
pH 7.6, 37C
-
0.0267
(pA)10
-
pH 7.6, 37C
0.0025
(pA)10*d(pT)10, (pA)11*d(pT)11
-
pH 7.6, 37C
-
0.03
(pA)12, (pA)16
-
pH 7.6, 37C
-
0.0025
(pA)16*d(pT)16
-
pH 7.6, 37C
-
0.263
(pA)2
-
pH 7.6, 37C
0.199
(pA)3
-
pH 7.6, 37C
0.183
(pA)4
-
pH 7.6, 37C
0.00759
(pA)4*d(pT)4
-
pH 7.6, 37C
-
0.1
(pA)6
-
pH 7.6, 37C
0.0214
(pA)6*d(pT)6
-
pH 7.6, 37C
-
0.0367
(pA)8
-
pH 7.6, 37C
0.0063
(pA)8*d(pT)8
-
pH 7.6, 37C
-
0.0269
(pA)9
-
pH 7.6, 37C
0.0447
(pC)10
-
pH 7.6, 37C
0.038
(pC)14
-
pH 7.6, 37C
-
0.316
(pC)2
-
pH 7.6, 37C
0.214
(pC)4
-
pH 7.6, 37C
0.12
(pC)6
-
pH 7.6, 37C
0.0708
(pC)8
-
pH 7.6, 37C
0.157
(pU)10
-
pH 7.6, 37C
0.01
(pU)10*(pA)10
-
pH 7.6, 37C
-
0.159
(pU)11
-
pH 7.6, 37C
-
0.158
(pU)16
-
pH 7.6, 37C
-
0.01
(pU)16*(pA)16
-
pH 7.6, 37C
-
0.7
(pU)4
-
pH 7.6, 37C
0.135
(pU)4*(pA)4
-
pH 7.6, 37C
-
0.339
(pU)6
-
pH 7.6, 37C
0.0166
(pU)6*(pA)6
-
pH 7.6, 37C
-
0.178
(pU)8
-
pH 7.6, 37C
0.158
(pU)9
-
pH 7.6, 37C
0.0167
(pU)9*(pA)9
-
pH 7.6, 37C
-
0.00018
1-methyl-4-[(1E)-1-[2-(6-methyl[1,3]dioxolo[4,5-g]quinolin-8-yl)hydrazinylidene]ethyl]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one
-
pH not specified in the publication, temperature not specified in the publication
0.00019
8-[(2E)-2-(3-methoxybenzylidene)hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
pH not specified in the publication, temperature not specified in the publication
0.00012
8-[(2E)-2-[(9-ethyl-9H-carbazol-3-yl)methylidene]hydrazinyl]-6-methyl[1,3]dioxolo[4,5-g]quinoline
-
pH not specified in the publication, temperature not specified in the publication
0.373
AMP
-
pH 7.6, 37C
0.447
CMP
-
pH 7.6, 37C
0.059
d(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))
-
pH 7.6, 37C
0.00166
d(pA)10
-
pH 7.6, 37C
0.00033
d(pA)10*d(pT)10
-
pH 7.6, 37C
-
0.0017
d(pA)12
-
pH 7.6, 37C
0.00036
d(pA)12*d(pT)12
-
pH 7.6, 37C
-
0.0017
d(pA)14
-
pH 7.6, 37C
0.00033
d(pA)14*d(pT)14
-
pH 7.6, 37C
-
0.00166
d(pA)16
-
pH 7.6, 37C
0.00033
d(pA)16*d(pT)16
-
pH 7.6, 37C
-
0.05
d(pA)2
-
pH 7.6, 37C
0.0366
d(pA)2*d(pT)2
-
pH 7.6, 37C
-
0.00033
d(pA)20*(pT)20
-
pH 7.6, 37C
-
0.033
d(pA)4
-
pH 7.6, 37C
0.0266
d(pA)4*d(pT)4
-
pH 7.6, 37C
-
0.0172
d(pA)6
-
pH 7.6, 37C
0.0118
d(pA)6*d(pT)6
-
pH 7.6, 37C
-
0.0025
d(pA)8
-
pH 7.6, 37C
0.0093
d(pA)8*d(pT)8
-
pH 7.6, 37C
-
0.0033
d(pC)10
-
pH 7.6, 37C
0.0033
d(pC)11, d(pC)13
-
pH 7.6, 37C
-
0.14
d(pC)2
-
pH 7.6, 37C
0.06
d(pC)3
-
pH 7.6, 37C
0.0217
d(pC)5
-
pH 7.6, 37C
0.01
d(pC)7
-
pH 7.6, 37C
0.0047
d(pC)9
-
pH 7.6, 37C
0.102
d(pG)2
-
pH 7.6, 37C
0.0383
d(pG)4
-
pH 7.6, 37C
0.0144
d(pG)6
-
pH 7.6, 37C
0.0054
d(pG)8
-
pH 7.6, 37C
0.0025
d(pT)10
-
pH 7.6, 37C
0.0025
d(pT)11, d(pT)12, d(pT)14
-
pH 7.6, 37C
-
0.00257
d(pT)15
-
pH 7.6, 37C
-
0.1166
d(pT)2
-
pH 7.6, 37C
0.0667
d(pT)3
-
pH 7.6, 37C
0.045
d(pT)4
-
pH 7.6, 37C
0.0246
d(pT)6
-
pH 7.6, 37C
0.0083
d(pT)8
-
pH 7.6, 37C
0.165
dAMP
-
pH 7.6, 37C
0.1633
dCMP
-
pH 7.6, 37C
0.1666
dGMP
-
pH 7.6, 37C
0.1633
dTMP
-
pH 7.6, 37C
0.0117
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))3pT]
-
pH 7.6, 37C
0.0052
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))5pT]
-
pH 7.6, 37C
0.0023
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))7pT]
-
pH 7.6, 37C
0.001
d[(p((3-hydroxytetrahydrofuran-2-yl)methyl phosphate))9pT]
-
pH 7.6, 37C
50
NaCl
-
-
0.36
NaH2PO4
-
pH 7.6, 37C
1.873
UMP
-
pH 7.6, 37C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016
2,2'-(2-oxo-1H-benzimidazole-1,3(2H)-diyl)diacetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.011
2,2'-(3,7-dioxo-5,7-dihydro-1H,3H-benzo[1,2-c:4,5-c']difuran-1,5-diyl)diacetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50 mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.008
2,2'-[(6-oxo-6H-benzo[c]chromene-1,3-diyl)bis(oxy)]dipropanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.019
2,2'-[(6-phenylpyrimidine-2,4-diyl)disulfanediyl]diacetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
2,2'-[butane-1,4-diylbis(1H-benzimidazole-2,1-diyl)]diacetic acid
Homo sapiens;
-
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0021
2,4,9-trimethylpyridino[2,3-b]quinoline-5-ylamine
Homo sapiens;
-
-
0.009
2-((Z)-2-oxo-3-(4-oxo-2-thioxothiazolidin-5-ylidene)indolin-1-yl)acetic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.008
2-(5-((2-(2-carboxyphenyl)-1,3-dioxo)-2,3-dihydro-1H-isoindol-5-yl)carbonyl-1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)benzoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
-
0.003
2-[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.017
3,3'-(1,3,4-thiadiazole-2,5-diyldisulfanediyl)dipropanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.015
3,3'-(2-thioxo-1H-benzimidazole-1,3(2H)-diyl)dipropanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.011
3-((3,4-dimethylphenoxy)methyl)furan-2-carboxylic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.027
3-((pyridin-2-ylthio)methyl)benzofuran-2-carboxylic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
3-(1-(carboxymethyl)-5-(4-chlorophenyl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.009
3-(1-(carboxymethyl)-5-(4-fluorophenyl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.009
3-(1-(carboxymethyl)-5-(thiophen-2-yl)-1H-pyrrol-2-yl)propanoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.012
3-(1-(carboxymethyl)-5-p-tolyl-1H-pyrrol-2-yl)propanoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
3-(2-carboxyethyl)-4-hydroxyquinoline-6-carboxylic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
3-(5-((E)-(3-(carboxymethyl)-4-oxo-2-sulfanylidene-1,3-thiazolidin-5-ylidene)methyl)furan-2-yl)benzoic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
3-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]propanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
3-[(6-amino-9H-purin-8-yl)sulfanyl]propanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 3 H-bond acceptors and 1 negative ionizable feature, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.015
3-[[4-(carboxymethyl)benzyl]sulfanyl]-8-methyl-5H-[1,2,4]triazino[5,6-b]indole-5-carboxylic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0064
4-((2,6,8-trimethylquinolin-4-yl)amino)phenol
Homo sapiens;
-
-
0.006
4-((2-carboxyphenoxy)methyl)-2,5-dimethylfuran-3-carboxylic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.01
4-(4-(4-carboxyphenoxy)phenylsulfonyl)benzene-1,2-dioic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
4-(4-(4-carboxyphenylsulfonyl)phenyl)sulfanylbenzene-1,2-dioic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. Then, 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.004
4-(4-(4-carboxyphenylthio)phenylsulfonyl)benzene-1,2-dioic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.02
4-([[(3-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-5-methylfuran-2-carboxylic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.012
4-[(4Z)-4-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-5-oxo-2-thioxoimidazolidin-1-yl]butanoic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.022
4-[[(2-carboxypropyl)sulfanyl]methyl]-5-methylfuran-2-carboxylic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.005
5,5'-[methanediylbis(sulfanediylmethanediyl)]bis(2-methylfuran-3-carboxylic acid)
Homo sapiens;
-
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.016
5-(((tetrahydrofuran-2-yl)methylthio)methyl)-2-methylfuran-3-carboxylic acid
Homo sapiens;
-
preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
5-([[(4-carboxy-5-methylfuran-2-yl)methyl]sulfanyl]methyl)-3-methylfuran-2-carboxylic acid
Homo sapiens;
-
small-molecule inhibitor containing 4 H-bond acceptors and 3 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0005
6-hydroxy-DL-DOPA
Homo sapiens;
-
IC50 less than 0.0005 mM
0.05
ceftriaxone sodium
Homo sapiens;
-
IC50 above 0.05 mM
0.05
cephapirin sodium
Homo sapiens;
-
IC50 above 0.05 mM
0.0005
mitoxanthrone
Homo sapiens;
-
IC50 less than 0.0005 mM
0.0005
myricetin
Homo sapiens;
-
IC50 less than 0.0005 mM
0.0016
N-(3-chlorophenyl)-5,6-dihydro-4H-cyclopenta[d]isoxazole-3-carboxamide
Homo sapiens;
-
-
0.0005
Reactive blue 2
Homo sapiens;
-
IC50 less than 0.0005 mM
0.011
[(3Z)-3-(3-[[(2-hydroxyphenyl)carbonyl]amino]-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.006
[(3Z)-3-[3-(4-bromophenyl)-4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene]-2-oxo-2,3-dihydro-1H-indol-1-yl]acetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.013
[(5Z)-5-[1-(carboxymethyl)-2-oxo-1,2-dihydro-3H-indol-3-ylidene]-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid
Homo sapiens;
-
small-molecule inhibitor containing 1 hydrophobic feature, 1 H-bond acceptor and 2 negative ionizable features, preincubation at a final concentration of 0.05 nM with the inhibitor in buffer (50mM NaCl, 1 mM HEPES, pH 7.5, 50 microM EDTA, 50 microM DTT, 10% glycerol, 7.5 mM MnCl2, 0.1 mg/ml bovine serum albumin, 10 mM 2-mercaptoethanol, 10% DMSO and 25 mM MOPS, pH 7.2) at 30C for 10 min. 200 nM of the 5'-end 32P-labeled linear oligonucleotide substrate is added
0.0017
[4-(2,5-dimethyl-1H-pyrrol-1-yl)phenoxy]acetic acid
Homo sapiens;
-
-
additional information
additional information
Homo sapiens;
-
The APE1 inhibitory profile of some of the most potent compounds indicates that along with two terminal fingerprint negatively ionizable features or bioisostere groups of negatively ionizable features, an optimum sized central hydrophobic core with or without a favorably substituted H-bond acceptor-donor functional group is essential for a compound being recognized by APE1 and inhibit its catalytic activity
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.003133
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.4 - 6.8
-
nucleotide incision repair activity
7
-
exonuclease assay, buffer B
7.2
-
assay at
7.4
-
AP endonuclease assay
7.5 - 8
-
-
7.8 - 8.2
-
AP endonuclease activity
8.5
-
assay at
9.2
-
AP-endonuclease assay
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.3
-
pH 7.5: 50% of maximal activity, pH 8.3: activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
assay at
23
-
electrophoretic mobility shift assay
30
-
assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
pH range 6-9
9.9
-
calculated from DNA sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
APE1 is highly expressed in selected regions of the central nervous system
Manually annotated by BRENDA team
increased nuclear expression of APE1 in neuronal and glial cells in both familial and sporadic Alzheimer
Manually annotated by BRENDA team
-
purified recombinant APE1 protein
Manually annotated by BRENDA team
-
human umbilical vein endothelial cells are infected with adenovirus encoding APE/Ref-1
Manually annotated by BRENDA team
-
APE-1 expression is mainly localized in epithelial cells within gastric adenoma
Manually annotated by BRENDA team
-
human gastric epithelial cell line AGS
Manually annotated by BRENDA team
-
fibroblasts
Manually annotated by BRENDA team
a reduction in APE1 expression, followed by an increase in the apoptotic rate, occurs in the hippocampus after a hypoxic-ischemic injury, patients with Alzheimer show an increased expression of APE1 levels in senile plaques and plaque-like structures
Manually annotated by BRENDA team
-
various cell lines, Bcl2, a major antiapoptotic and/or oncogenic protein, is found to co-express with APE1 in H69 and H460 but not in other tested lung cancer cells
Manually annotated by BRENDA team
-
wm3211, wm1205, c83-2c, c81-46A, A375, c81-61
Manually annotated by BRENDA team
-
APE-1 expression in gastric cancer tissues
Manually annotated by BRENDA team
-
Helicobacter pylori (CagA+) water-extract protein (HPWEP)-stimulated
Manually annotated by BRENDA team
-
APE1 protein is elevated in 72% of the tissues and among those with a known clinical outcome. There is a significant correlation between high APE1 expression levels and reduced survival times
Manually annotated by BRENDA team
-
human prostate cancer cell line
Manually annotated by BRENDA team
-
nuclear expression of APE1 in epidermal layers is markedly up-regulated in psoriatic skin, APE1 is essential for the transcriptional activation and nuclear translocation of hypoxia-inducible factor-1alpha and NF-kappaB
Manually annotated by BRENDA team
reduction in APE1 expression after ischemia
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
PDB
SCOP
CATH
UNIPROT
ORGANISM
Homo sapiens;
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33570
-
calculated from DNA sequence
35420
-
calculated by the ExPASy Prot Param tool and confirmed by SDS-PAGE
35470
-
calculated from amino acid sequence
37000 - 38000
-
SDS-PAGE
50000
-
determined by SDS-PAGE and Western blotting
53000
SDS-PAGE
60000
-
fusion protein with glutathione S-transferase
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
dimer removal is not affected by Pb2+, Cr6+, Fe3+ or Sn3+
monomer
additional information
These two biological activities are located in two functionally distinct domains. The n-terminus, containing the nuclear localization signal region, is principally devoted to the redox activity, through Cys65, while the c-terminus exerts the enzymatic activity on the abasic sites of DNA.
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
acetylation
phosphoprotein
proteolytic modification
Proteolysis occurring at residue Lys31, this post-translational regulation of APE1 protein is responsible for enhanced cell death mediated by granzyme A and granzyme K. Truncated APE1 looses its AP-endonuclease activity and acquire a nonspecific DNAse function.
S-nitrosation
2 of the 7 Cys residues (Cys93 and Cys310) of APE1 undergoes S-nitrosation in response to nitric oxide stimulation, leading to nucleus to cytoplasm relocalization of the protein in a CRM1-independent process, possibly as a consequence of demasking a putative nuclear export signal
sumoylation
high probability, putative sumoylation site, which contains a canonical sumoylation K-X-D/E motif, addition of a small ubiquitin-like modifier (SUMO) molecule to the target protein accounts for an increase of 12 kDa of the apparent molecular mass of the target protein. The effects of posttranslational modification by SUMO to compete for target lysines enhance or inhibit interactions with other proteins (or other binding partners such as DNA) or induce conformational changes.
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
molecular modeling of inhibitors to crystal structure, PDB entry 1DE8
-
mutant C65A hApe1 protein is diluted to 10 mg/ml in 10 mM HEPES pH 7.5 and then crystallized by hanging drop vapor diffusion using 10 mM MES pH 6.0, 7.5 mM Sm(OAc)3, 4% dioxane, 10-20% PEG 8000 as the precipitating solution at 20C. The structure is solved at a resolution of 33.0-1.9 A
-
to 1.92 A resolution with a single Mg2+ ion in the active site. The structure reveals ideal octahedral coordination of Mg2+ via two carboxylate groups and four water molecules. One residue that coordinates Mg2+ directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
lowering the pH to 4.5 simply protonated H309 and makes it unsuitable for metal binding
692773
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
under base excision repair conditions, the REF1 domain of APE1 influences the stability of both the enzyme-substrate and enzyme-product complexes, as well as the isomerization rate, but does not affect the rates of initial complex formation or catalysis
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-4C, 10 months, 50% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
according to protocols for purification of GFP-, GST- and His-tagged proteins
-
after affinity purification and cleavage of the His-tag, the untagged proteins to near homogeneity are purified by fast protein liquid chromatography using heparin-sepharose
-
APE-1 proteins partially purified purified are visualized by Western blot using anti-human APE-1 antibody
-
Bacteria are lyzed in a denaturing buffer (50 mmol NaCl and phosphate pH 7.5, 4 mol urea), the His-hNTH1 protein is purified by chromatography on a nickel column followed by gel filtration on a Superdex-200 column. The TAP-hNTH1 protein is purified from a stable MCF-7 clone expressing this protein construct with a TAP purification kit.
-
by ammonium sulfate precipitation and affinity chromatography, using a HiTrap chelating column, charged with Ni2+, and a HiTrap heparin column
-
Clear supernatant from cell extract is applied to two columns in series: a strong anion exchange column (Q-Sepharose) followed by a strong cation exchange (HS50). After sample loading, both columns are washed with buffer and then the Q-Sepharose column is disconnected. APE1 bound in the HS50 column is eluted with a 50-700 mM KCl gradient. Clean APE1 fractions are pooled and then dialyzed extensively in buffer to remove glycerol, elution salts, and metal ions, followed by two runs of dialysis with EDTA-free buffer. Average yield of APE1 is 200 mg out of 15 g of cells
-
full-length recombinant CSB and APE1 proteins are expressed and purified, used in direct and indirect ELISAs
-
His-tagged APE1 is purified from Escherichia coli M15 cells by using Ni-affinity chromatography with Swell-gel Nickel-chelated discs
-
histidine-tagged AP endonucleases are purified on Ni2+-charged HiTrap Chelating HP columns
-
homogeneity
-
Ni-NTA column chromatography and Superdex 75 gel filtration
-
Ni-NTA column chromatography, S-Sepharose column chromatography
-
Ni-NTA column chromatography, SP-Sepharose column chromatography
-
nickel-Sepharose resin column chromatography, gel filtration
-
partial, endonuclease A
-
Purification is done using the standard glutathione affinity purification protocol. The C65A mutant is purified as follows: cell suspension is centrifuged, supernatant is loaded on a Ni-NTA column and the protein is eluted with a linear imidazole gradient. Fractions containing C65A hApe1 are further purified on an S-Sepharose column with a linear NaCl gradient.
-
recombinant
-
recombinant human full-length and Ndelta33 APE1 is purified using a Ni-NTA Superflow and a SP-Sepharose column
-
RKO cell protein is extracted
-
wild-type and mutant enzymes H270A, H270R, H270L, Q315A, F319A
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
adenoviruses full-length APE1/Ref-1 (AdAPE1/Ref-1) is generated by homologous recombination in human embryonic kidney 293 cells. Human umbilical vein endothelial cells are infected with 200 multiplicity of infection
-
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Escherichia coli Rosetta cells
-
expression in Escherichia coli
-
fusion protein with glutathione S-transferase
Generation of random mutations in the ape1 gene and selection of variants that confer protection against H2O2. Random library of ape1 mutants is generated by transforming the mutator strain XL1-Red with the prokaryotic ape1 plasmid pKK-ape1. The H2O2-resistant phenotype (mutant D70A) is expressed in Escherichia coli strain BW528 (xth nfo), which is deficient in the major AP endonucleases, exonuclease III and endonuclease IV
-
His-tagged APE1 is expressed in Escherichia coli M15 cells
-
Human Ape1/Ref-1 cDNA is amplified by RT-PCR using Ape1/Ref-1-specific primers and from human GM00637 fibroblasts. AP endonuclease domain deletion mutant deltaAPD is amplified by RT-PCR using specific primers from full length human Ape1/Ref-1 cDNA. Redox domain deletion mutant deltaRD is amplified by RT-PCR using specific primers from full length human Ape1/Ref-1 cDNA.
-
into the pET-14b vector
-
into the pET15b vector for expression in Escherichia coli
-
into the pET15b vector for expression in Escherichia coli BL21DE3 cells
-
into the pET28b+ vector for expression in Escherichia BL21DE3 RIL cells
-
into the pSLV vector to generate pSLX-APE-Myc
-
into various expression plasmids for GFP, GST or His-tag, for expression in Escherichia coli cells
-
Recombinant human APE1 protein is overexpressed from clone pETApe1 in Escherichia coli BL21(DE3)
-
RKO cell lines are established, that can be induced by doxycycline to overexpress APE-1 wild-type, mutant C65A, mutant E96A or mutant E96Q
-
the APE-1/Ref-1 expression vector pFLAG-APE-1 cDNA3.1 is prepared
-
The human NTH1 cDNA is cloned into the PCRII plasmid and it is cloned into the EcoRI site of the pGEX-2TK vector. The hNTH1 cDNA is cut (amino acids 1-94) and cloned into the modified restriction sites in the pGEX-2TK vector. The remaining fragment (amino acids 95-312) is cloned into the pGEX-3X vector. The hNTH1 cDNA is cloned into the pET24d vector in-frame with the His-tag and into the pNTAP-B vector in-frame with the TAP-epitope. To knock down the expression of Y-box-binding protein-1, a hairpin sequence specific to Y-box-binding protein-1 is cloned into the pSuper vector. His-hNTH1 protein is produced in the BL21 bacterial strain. MCF-7 cells are transfected with a siRNA specific to hNTH1.
-
The wild-type and mutant hApe1 proteins are expressed as GST-fusions in Escherichia coli
-
wild-type APE1 and its Cys mutants are expressed as His-tag fusion polypeptides in Escherichia coli
-
wild-type APE1 encoding full-length of APE1 and APE1 C65A/C93A encoding mutant form of APE1 in pCMVTag2B mammalian expression vector are generated by standard cloning method. TAT-APE1 is generated by insertion of full-length of APE1 into pTAT-2.1
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
APE1 expression is up-regulated in psoriatic epidermis
-
Helicobacter pylori infection induces apoptosis and increases APE-1 expression in human gastric epithelial cells
-