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Information on EC 4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase and Organism(s) Pyrobaculum aerophilum and UniProt Accession Q8ZVK6

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EC Tree
     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.99 Other carbon-oxygen lyases
                4.2.99.18 DNA-(apurinic or apyrimidinic site) lyase
IUBMB 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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Pyrobaculum aerophilum
UNIPROT: Q8ZVK6
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Word Map
The taxonomic range for the selected organisms is: Pyrobaculum aerophilum
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
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
archaeal GO glycosylase
-
Pa-AGOG
bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
Pa-AGOG DNA glycosylase
bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity)
PAE2237
locus name
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
-
-
-
-
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
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
DNA with an abasic site
?
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
DNA with an abasic site
?
show the reaction diagram
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates
-
-
?
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
9.2
calculated from sequence
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme is part of the base excision repair (BER) pathway. It protects from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine, from single- and double-stranded DNA substrates. Bifunctional enzyme that catalyzes the excision of 8-oxoguanine by cleaving the N-glycosylic bond between the base and the deoxyribose moiety (glycosylase activity) and subsequently cleave the DNA backbone (lyase activity, EC 4.2.99.18)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29467
x * 29467, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 29467, calculated from sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of the enzyme and that of its complex with 8-oxo-guanosine at 1.0 and 1.7 A resolution, respectively, are grown by sitting drops method
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D166N
mutant enzyme shows wild-type activity
D172N
D172Q
K140Q
K147Q
activity of mutant enzyme is severely attenuated
Q31E/D218S
almost no glycosylase activity
Q31S
significantly reduced glycosylase activity
W222A
almost no glycosylase activity
W222F
mutant is similarly active as wild type on 8-oxoguanine/C substrates
W69F
mutant is similarly active as wild type on 8-oxoguanine/C substrates
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
78
Tm-value for mutant enzyme W69F
80
15 min, no notable effect on catalytic activity
84
Tm-value for mutant enzyme D172Q
86
Tm-value for mutant enzyme Q31S
88
Tm-value for mutant enzyme W222F
93
Tm-value for wild-type enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lingaraju, G.M.; Prota, A.E.; Winkler, F.K.
Mutational studies of Pa-AGOG DNA glycosylase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum
DNA Repair
8
857-864
2009
Pyrobaculum aerophilum (Q8ZVK6), Pyrobaculum aerophilum, Pyrobaculum aerophilum DSM 7523 (Q8ZVK6)
Manually annotated by BRENDA team
Sartori, A.A.; Lingaraju, G.M.; Hunziker, P.; Winkler, F.K.; Jiricny, J.
Pa-AGOG, the founding member of a new family of archaeal 8-oxoguanine DNA-glycosylases
Nucleic Acids Res.
32
6531-6539
2004
Pyrobaculum aerophilum (Q8ZVK6), Pyrobaculum aerophilum, Pyrobaculum aerophilum DSM 7523 (Q8ZVK6)
Manually annotated by BRENDA team
Lingaraju, G.M.; Sartori, A.A.; Kostrewa, D.; Prota, A.E.; Jiricny, J.; Winkler, F.K.
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure
Structure
13
87-98
2005
Pyrobaculum aerophilum (Q8ZVK6), Pyrobaculum aerophilum, Pyrobaculum aerophilum DSM 7523 (Q8ZVK6)
Manually annotated by BRENDA team