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Information on EC 4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P22936
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4.2.99.18 DNA-(apurinic or apyrimidinic site) lyaseIUBMB Comments
'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.
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Word Map
- 4.2.99.18
- strand
-
exonuclease
- glycosylases
-
single-stranded
- pyrimidine
- endonucleases
- 8-oxoguanine
- nick
- thymine
- uracil
- duplex
-
genotoxic
- xrcc1
-
phosphodiester
- comet
- deoxyribose
- methanesulfonate
- mispairs
-
uracil-dna
-
depurinated
-
beta-elimination
-
excise
- formamidopyrimidine
-
3'-phosphatase
- 7,8-dihydro-8-oxoguanine
- tetrahydrofuran
-
site-containing
-
mutyh
-
endonucleolytic
-
xeroderma
- pigmentosum
-
base-excision
- 3'-phosphodiesterase
-
cross-complementing
- 8-oxo-7,8-dihydroguanine
- fen1
-
unrepaired
-
formamidopyrimidine-dna
-
incises
-
long-patch
-
dna-repair
-
uracil-containing
-
ser326cys
- dihydrouracil
-
arg399gln
- 3'-exonuclease
-
reduction-oxidation
-
enzyme-dna
- medicine
-
gap-filling
-
damage-specific
- analysis
- diagnostics
- biotechnology
- drug development
- pharmacology
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
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
Synonyms
ap endonuclease, ref-1, ape1/ref-1, apex1, ape/ref-1, apurinic/apyrimidinic endonuclease 1, ap lyase, ape-1, alkbh1, endo iii, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AP 1
-
-
-
-
AP Dnase
-
-
-
-
AP endo
-
-
-
-
AP endonuclease
-
-
-
-
AP endonuclease Class I
-
-
-
-
AP lyase
-
-
-
-
AP-endonuclease
-
-
-
-
Ape
-
-
-
-
APEN
-
-
-
-
APEX nuclease
-
-
-
-
APN1
-
-
-
-
apurinic DNA endonuclease
-
-
-
-
apurinic endodeoxyribonuclease
-
-
-
-
apurinic endonuclease
-
-
-
-
apurinic-apyrimidinic DNA endonuclease
-
-
-
-
apurinic-apyrimidinic endodeoxyribonuclease
-
-
-
-
apurinic-apyrimidinic endonuclease
-
-
-
-
apurinic/apyrimidinic lyase
-
-
-
-
apurinic/apyrimidinic specific endonuclease
-
-
-
-
apyrimidinic endonuclease
-
-
-
-
class II apurinic/apyrimidinic(AP)-endonuclease
-
-
-
-
deoxyribonuclease (apurinic or apyrimidinic)
-
-
-
-
E. coli endonuclease III
-
-
-
-
endodeoxyribonuclease
-
-
-
-
endodeoxyribonuclease III
-
-
-
-
endonuclease III
endonuclease VI
-
-
-
-
Escherichia coli endonuclease III
-
-
-
-
HAP1
-
-
-
-
HAP1h
-
-
-
-
Micrococcus luteus UV endonuclease
-
-
-
-
MMH
-
-
-
-
Nfo
-
-
-
-
Ntg1p
-
-
-
-
Ntg2p
-
-
-
-
NTH1
-
-
-
-
nuclease, apurinic endodeoxyribo-
-
-
-
-
nuclease, apurinic-apyrimidinic endodeoxyribo-
-
-
-
-
nuclease, endodeoxyribo-, III
-
-
-
-
phage-T4 UV endonuclease
-
-
-
-
REF-1 protein
-
-
-
-
Ref1
-
-
-
-
UV endo V
-
-
-
-
UV endonuclease
-
-
-
-
UV endonuclease V
-
-
-
-
endonuclease III
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
60184-90-9
-
61811-29-8
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
?
-
-
-
-
?
DNA
fragments of DNA
-
cleaves all four types of abasic site-containing substrates: AP/G, AP/A, AP/C, AP/T, with a moderate preference for AP/T sites
-
?
DNA
fragments of DNA
-
cuts the DNA strands on the 5' side of the apurinic sites giving a 3'-OH and a 5'-phosphate
-
?
DNA
fragments of DNA
-
catalyzes the hydrolysis of the 5'-phosphodiester bond at the abasic site
-
?
DNA
fragments of DNA
-
recognizes and cleaves DNA substrates containing dihydrouracil, 2,6-diamino-4-hydroxy-5N-methylformamidopyrimidine and abasic sites, but not DNA substrates containing uracil or 8-oxoguanine
-
?
DNA
fragments of DNA
-
DNA containing dihydrouridine, 5,3-dihydrothymidine, 5-hydroxy-2'-deoxyuridine, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine or tetrahydrofuranyl
-
?
DNA
fragments of DNA
-
oxidative DNA damage is primarily reversed by the base excision repair pathway, initiated by N-glycosylase apurinic/apyrimidinic lyase proteins
-
-
ir
additional information
?
-
the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
-
-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized and purified, a fluorescent 2-aminopurine (2-aPu) probe is located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran) by wild-type and mutant H83A enzymes, overview
-
-
?
additional information
?
-
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized and purified, a fluorescent 2-aminopurine (2-aPu) probe is located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran) by wild-type and mutant H83A enzymes, overview
-
-
?
additional information
?
-
substrate oligodeoxyribonucleotides (ODNs) are synthesized with a fluorescent 2-aminopurine (2-aPu) probe located either on the 5'- or 3'-side of an abasic site. Cleavage of substrates AP(2-aPu) and F(2-aPu) (F = tetrahydrofuran) in presence of Zn2+ and Mg2+ by wild-type and mutant H83A enzymes, overview. Molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. The DNA substrate structure affects nucleotide incision repair (NIR) catalysis. Location of the 2-aPu residue near DHU decreases the efficacy of NIR activity of the WT enzyme and of H83A Apn1: nucleotide incision repair (NIR) activity of both enzymes decreases in the following descending order of substrates: DHU, DHU(2-aPu), and (2-aPu)DHU. Apn1 cannot incise the (2-aPu)DHU duplex because of the spatial structure of the (2-aPu)DHU-Apn1 complex, which is probably significantly distorted in the vicinity of the active site because two noncanonical base pairs are placed in close proximity to each other, the access of catalytically active amino acid residues and Zn2+ ions to the 5'-phosphodiester bond to be incised (located between the 2-aPu and DHU residues) might be blocked
-
-
?
additional information
?
-
-
enzyme also has DNA N-glycosylase activity
-
-
?
additional information
?
-
-
ntg1 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
additional information
?
-
-
ntg2 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DNA
fragments of DNA
-
-
-
-
?
DNA
fragments of DNA
-
oxidative DNA damage is primarily reversed by the base excision repair pathway, initiated by N-glycosylase apurinic/apyrimidinic lyase proteins
-
-
ir
additional information
?
-
the nucleotide incision repair (NIR) recruiting Saccharomyces cerevisiae Apn1 proceeds via multistep rearrangements of the complex of Apn1 with a DHU-containing DNA substrate and results in the incised product of the reaction
-
-
?
additional information
?
-
-
ntg1 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
additional information
?
-
-
ntg2 possesses N-glycosylase/AP lyase activity that allows recognition and repair of oxidative base damage (primarily of pyrimidines) as well as abasic sites
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
Mg2+
NaCl
additional information
the nucleotide incision repair of the enzyme in presence of Mg2+ is unaltered, Mg2+ does not affect yeast Ape1 activity
Zn2+
His83 coordinates one of three Zn2+ ions in Apn1's active site, structure comparisons. Structure of enzyme mutant H83A Apn1-substrate DNA complex with three Zn2+ ions containing Zn2+ ions per molecule of mutant enzyme, overview. Zn2+ ions are involved in catalysis
Zn2+
required for catalysis, molecular dynamics. The active site of H83A Apn1 contains only two Zn2+ ions, with their positions being changed versus a trinuclear Zn2+ cluster of wild-type Apn1
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00005
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
0.000026
DNA containing 5-hydroxy-2'-deoxyuridine/G
-
pH 7.5, 37°C
-
additional information
additional information
measurement of conformational dynamics of DNA at pre-steady-state conditions, stopped-flow measurements. Rate and equilibrium constants for wild-type enzyme and mutant H83A Apn1 interactions with DNA substrates F(2-aPu) and AP(2-aPu), F is tetrahydrofuran
-
additional information
additional information
-
measurement of conformational dynamics of DNA at pre-steady-state conditions, stopped-flow measurements. Rate and equilibrium constants for wild-type enzyme and mutant H83A Apn1 interactions with DNA substrates F(2-aPu) and AP(2-aPu), F is tetrahydrofuran
-
additional information
additional information
stopped-flow fluorescence measurements, kinetic analysis of nucleotide incision repair (NIR) pathway compared to base excision DNA repair (BER) pathway. Rate constants of wild-type Apn1 interaction with substrate DHU(2-aPu), overview. Proposed kinetic mechanisms, containing two or three binding steps, for the interaction of wild-type Apn1 with substrate DHU(2-aPu)
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0117
DNA containing 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine/C
-
pH 7.5, 37°C
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.4
activity assay, oligonucleotide cleavage assay, endonuclease and 3'-phosphodiesterase activity is measured
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
activity assay, oligonucleotide cleavage assay, endonuclease and 3'-phosphodiesterase activity is measured
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
-
localization of Ntg1 is dynamically regulated in response to nuclear and mitochondrial oxidative stress
-
-
sumoylated Ntg1 accumulates in the nucleus following oxidative stress
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
additional information
physiological function
apurinic/apyrimidinic endonuclease Apn1 of Saccharomyces cerevisiae is known as a key player of the base excision DNA repair (BER) pathway in yeast. BER is initiated by DNA glycosylases, whereas Apn1 can start DNA repair individually in the nucleotide incision repair (NIR) pathway. More delicate regulation of Apn1's NIR activity is necessary due to the more complicated kinetic mechanism, as compared to BER
physiological function
the apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA
additional information
molecular dynamics simulations elucidates the structural features of complexes of the enzyme with DHU-containing DNAs. Enzyme three-dimensional structure homology modeling using the structure of Endo IV (PDB ID 1QTW) as template
additional information
residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
additional information
-
residue His83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Substrate binding structure analysis using DNA duplex crystal structure (PDB ID 2NQJ) for molecular dynamics simulations
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40500
Western Blots showing Apn1 expression in purified nuclear, mitochondrial extracts and whole cell lysates
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
sumoylation
sumoylation
-
modification with the ubiquitin-like SUMO protein, is associated with targeting of Ntg1 to nuclei containing oxidative DNA damage, lysine 364 within the sequence KREL is most likely to be sumoylated among the 36 lysines present in Ntg1
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H83A
additional information
-
deletion mutant delta369 and delta491, the C-terminal deletion does not affect the AP endonuclease activity, but the protein is defective in the removal of AP sites in vivo
H83A
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. Analysis of kinetics of recognition, binding, and incision of DNA substrates of the H83A Apn1 mutant. Substitution of His83 with Ala influences catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. H83A Apn1 appears to cleave substrates AP(2-aPu) and F(2-aPu) in several stages (F is tetrahydrofuran). Minimal kinetic mechanism of abasic site cleavage by H83A Apn1, molecular dynamics of H83A Apn1, overview. Molecular dynamics simulations of the H83A Apn1 structure containing the two Zn2+ ions reveal an insignificant movement of Zn2 relative to DNA and amino acid residues involved in Zn2 coordination. Structure of enzyme mutant H83A Apn1-substrate DNA complex with three Zn2+ ions containing Zn2+ ions per molecule of mutant enzyme, overview
H83A
site-directed mutagenesis, the mutation decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis, suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. The active site of H83A Apn1 contains only two Zn2+ ions, with their positions being changed versus a trinuclear Zn2+ cluster of wild-type Apn1
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes by nickel affinity chromatography
TAP-tagged Ntg1 is purified by a modified TAP method. To purify GST-tagged Ntg1, glutathione-Sepharose 4 Fast Flow beads are applied
-
TAP-tagged Ntg2 is purified by a modified TAP method. To purify GST-tagged Ntg2, glutathione-Sepharose 4 Fast Flow beads are applied
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene APN1, sequence comparisons, recombinant expression of His-tagged wild-type and mutant enzymes
the yeast apurinic/apyrimidinic endonuclease gene is cloned into the pcDNA3.neo plasmid for transfection of rat RCSN-3 cells
The pPS904 green fluorescent protein (GFP) expression vector (2m URA3) is employed for generation of C-terminally tagged Ntg1-GFP fusion protein. The Saccharomyces cerevisiae haploid strain FY86 is utilized for all localization studies. NTG1 strain (DSC0282) is generated by precisely replacing the NTG1 open reading frame in FY86 with the kanamycin antibiotic resistance gene. Haploid yeast strain expresses integrated genomic copies of C-terminally tandem affinity purification (TAP)-tagged Ntg1. Cells expressing galactose-inducible SMT3-HA and Ntg1-GST (DSC0221) are generated by integrating the hemagglutinin tag from the vector p1375 and the GAL promoter and glutathione S-transferase (GST) tag from the vector p2245 at the C-termini of the SMT3 and NTG1 products in the haploid strain ACY737.
-
The pPS904 green fluorescent protein (GFP) expression vector (2m URA3) is employed for generation of C-terminally tagged Ntg2-GFP fusion protein. The Saccharomyces cerevisiae haploid strain FY86 is utilized for localization studies. NTG2 strain (DSC0283) is generated by precisely replacing NTG2 open reading frame in FY86 with the kanamycin antibiotic resistance gene. Haploid yeast strain expresses integrated genomic copies of C-terminally tandem affinity purification (TAP)-tagged Ntg2. Cells expressing galactose-inducible Smt3-HA and Ntg2-GST (DSC0222) are generated by integrating the hemagglutinin tag from the vector p1375 and the GAL promoter and glutathione S-transferase (GST) tag from the vector p2245 at the C-termini of the SMT3 and NTG2 products in the haploid strain ACY737.
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
Apn1 could be used as a possible treatment strategy for attenuating or slowing down the pathogenesis of neurodegenerative diseases
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Foury, F.
Endonucleases in yeast mitochondria: apurinic and manganese-stimulated deoxyribonuclease activities in the inner mitochondrial membrane of Saccharomyces cerevisiae.
Eur. J. Biochem.
124
253-259
1982
Saccharomyces cerevisiae, Saccharomyces cerevisiae D273-10B/A1
Armel, P.R.; Wallace, S.S.
DNA repair in Saccharomyces, purification and characterization of apurinic endonuleases
J. Bacteriol.
160
895-902
1984
Saccharomyces cerevisiae
Ishchenko, A.A.; Sanz, G.; Privezentzev, C.V.; Maksimenko, A.V.; Saparbaev, M.
Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases
Nucleic Acids Res.
31
6344-6353
2003
Saccharomyces cerevisiae, Escherichia coli
Meadows, K.L.; Song, B.; Doetsch, P.W.
Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function
Nucleic Acids Res.
31
5560-5567
2003
Saccharomyces cerevisiae
Unk, I.; Haracska, L.; Johnson, R.E.; Prakash, S.; Prakash, L.
Apurinic endonuclease activity of yeast Apn2 protein
J. Biol. Chem.
275
22427-22434
2000
Saccharomyces cerevisiae
You, H.J.; Swanson, R.L.; Doetsch, P.W.
Saccharomyces cerevisiae possesses two functional homologues of Escherichia coli endonuclease III
Biochemistry
37
6033-6040
1998
Saccharomyces cerevisiae
Ho, R.; Rachek, L.I.; Xu, Y.; Kelley, M.R.; LeDoux, S.P.; Wilson, G.L.
Yeast apurinic/apyrimidinic endonuclease Apn1 protects mammalian neuronal cell line from oxidative stress
J. Neurochem.
102
13-24
2007
Saccharomyces cerevisiae (P22936)
Agger, S.A.; Lopez-Gallego, F.; Hoye, T.R.; Schmidt-Dannert, C.
Identification of sesquiterpene synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. strain PCC 7120
J. Bacteriol.
190
6084-6096
2008
Saccharomyces cerevisiae
Dyakonova, E.S.; Koval, V.V.; Lomzov, A.A.; Ishchenko, A.A.; Fedorova, O.S.
The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA
Biochim. Biophys. Acta
1850
1297-1309
2015
Saccharomyces cerevisiae (P22936), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 / S288c (P22936)
Dyakonova, E.S.; Koval, V.V.; Lomzov, A.A.; Ishchenko, A.A.; Fedorova, O.S.
Apurinic/apyrimidinic endonuclease Apn1 from Saccharomyces cerevisiae is recruited to the nucleotide incision repair pathway Kinetic and structural features
Biochimie
152
53-62
2018
Saccharomyces cerevisiae (P22936), Saccharomyces cerevisiae ATCC 204508 / S288c (P22936)
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