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Information on EC 3.2.2.23 - DNA-formamidopyrimidine glycosylase and Organism(s) Lactococcus lactis and UniProt Accession P42371

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     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.23 DNA-formamidopyrimidine glycosylase
IUBMB Comments
May play a significant role in processes leading to recovery from mutagenesis and/or cell death by alkylating agents. Also involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA.
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Lactococcus lactis
UNIPROT: P42371
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The taxonomic range for the selected organisms is: Lactococcus lactis
The enzyme appears in selected viruses and cellular organisms
Synonyms
neil1, neil3, fpg protein, formamidopyrimidine-dna glycosylase, formamidopyrimidine dna glycosylase, 8-oxoguanine-dna glycosylase, formamidopyrimidine glycosylase, fapy-dna glycosylase, fpg-1, fpg-l, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
formamidopyrimidine DNA glycosylase
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2,6-diamino-4-hydroxy-5(N-methyl)formamidopyrimidine-DNA glycosylase
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2,6-diamino-4-hydroxy-5N-formamidopyrimidine-DNA glycosylase
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2,6-diamino-4-hydroxy-5N-methyl-formamidopyrimidine-DNA glycosylase
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8-hydroxyguanine endonuclease
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8-oxoguanine DNA glycosylase
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deoxyribonucleate glycosidase
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DNA glycohydrolase (releasing 2,6-diamino-4-hydroxy-5-(N-methyl)-formamidopyrimidine)
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Fapy DNA glycosylase
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Fapy-DNA glycosylase
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formamidopyrimidine-DNA glycosyl hydrolase
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formamidopyrimidine-DNA glycosylase
Fpg protein
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glycosidase, deoxyribonucleate formamidopyrimidine
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of N-glycosyl bond
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SYSTEMATIC NAME
IUBMB Comments
DNA glycohydrolase [2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide releasing]
May play a significant role in processes leading to recovery from mutagenesis and/or cell death by alkylating agents. Also involved in the GO system responsible for removing an oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine) from DNA.
CAS REGISTRY NUMBER
COMMENTARY hide
78783-53-6
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
DNA + H2O
?
show the reaction diagram
DNA containing 8-hydroxyguanine residues + H2O
8-hydroxyguanine + DNA
show the reaction diagram
DNA containing 8-oxoguanine residues + H2O
DNA + 8-oxoguanine
show the reaction diagram
best substrate
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-
?
DNA containing formamidopyrimidine-guanine residues + H2O
4,6-diamino-5-formamidopyrimidine + DNA
show the reaction diagram
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?
DNA containing methylated formamidopyrimidine-guanine residues + H2O
2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine + DNA
show the reaction diagram
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?
DNA containing oxoG opposite C or A + H2O
2,6-diamino-4-hydroxy-5-formamidopyrimidine + DNA
show the reaction diagram
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-
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?
DNA containing ring-opened N7-methylguanine residues + H2O
2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine + DNA
show the reaction diagram
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?
DNA + H2O
?
show the reaction diagram
DNA containing 2,6-diamino-4-hydroxy-5-formamidopyrimidine residues + H2O
2,6-diamino-4-hydroxy-5-formamidopyrimidine + DNA
show the reaction diagram
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?
DNA containing 5-hydroxy-5-methylhydantoin residues opposite cytosine + H2O
5-hydroxy-5-methylhydantoin + DNA
show the reaction diagram
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excellent substrate when the lesion is opposite a cytosine, poor substrate when the lesion is opposite a adenine
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?
DNA containing 7-hydro-8-oxoguanine residues + H2O
DNA + 7-hydro-8-oxoguanine
show the reaction diagram
DNA containing 8-oxo-7,8-dihydropurine + H2O
8-oxo-7,8-dihydropurine + DNA
show the reaction diagram
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poor substrate when the lesion is opposite a cytosine
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?
additional information
?
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the enzyme is a DNA glycosylase/AP lyase specific for oxidized purines such as 8-oxo-7,8-dihydropurines and imidazole-ring opened purines (2,6-diamino-4-hydroxy-5-formamidopyrimidine and formamidopyrimidine derived from adenine)
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?
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 + H2O
?
show the reaction diagram
important role in protecting DNA against oxidative free radicals and reactive oxygen-derived species
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?
DNA containing 8-oxoguanine residues + H2O
DNA + 8-oxoguanine
show the reaction diagram
best substrate
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?
DNA + H2O
?
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
DNA containing 2-deoxyribonolactone residues
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suicide inhibitor for formamidopyrimidine-DNA glycosylase
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DNA containing 5-hydroxy-5-methylhydantoin residues
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suicide inhibitor for formamidopyrimidine-DNA glycosylase
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30000
active form
31300
1 * 31300, calculated from the amino acid sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
dynamic simulation of the pre-catalytic complex of Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. Only one transition is observed in the experimental reaction rate pH dependence plots, and Glu2 keeps the same set of interactions regardless of its protonation state. The adenine base opposite oxoG is highly distorting for the adjacent nucleotides. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tend to withdraw from their positions if A is opposite to the lesion
crystal structure of enzyme bound to a 1,3-propanediol abasic site analogue-containing DNA
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molecular dynamics study based on X-ray structure of enzyme bound to an abasic site analog-containing DNA
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme, overexpressed in Escherichia coli BH410
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
fpg-L gene is cloned, sequenced and overexpressed in Escherichia coli BH410, expression in Escherichia coli fpg and mutY mutants suppresses their spontaneous GC-TA mutator phenotype
expressed in Escherichia coli strain BH540
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Serre, L.; Pereira de Jesus, K.; Boiteux, S.; Zelwer, C.; Castaing, B.
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA
EMBO J.
21
2854-2865
2002
Lactococcus lactis
Manually annotated by BRENDA team
Duwat, P.; de Oliveira, R.; Ehrlich, S.D.; Boiteux, S.
Repair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein
Microbiology
141
411-417
1995
Lactococcus lactis (P42371), Lactococcus lactis
Manually annotated by BRENDA team
Amara, P.; Serre, L.; Castaing, B.; Thomas, A.
Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics
Protein Sci.
13
2009-2021
2004
Geobacillus stearothermophilus, Lactococcus lactis
Manually annotated by BRENDA team
Le Bihan, Y.V.; Angeles Izquierdo, M.; Coste, F.; Aller, P.; Culard, F.; Gehrke, T.H.; Essalhi, K.; Carell, T.; Castaing, B.
5-Hydroxy-5-methylhydantoin DNA lesion, a molecular trap for DNA glycosylases
Nucleic Acids Res.
39
6277-6290
2011
Lactococcus lactis
Manually annotated by BRENDA team
Prakash, A.; Doublie, S.; Wallace, S.S.
The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage
Prog. Mol. Biol. Transl. Sci.
110
71-91
2012
Escherichia coli (P05523), Geobacillus stearothermophilus (P84131), Lactococcus lactis (P42371), Thermus thermophilus (O50606), Thermus thermophilus DSM 579 (O50606)
Manually annotated by BRENDA team
Popov, A.V.; Endutkin, A.V.; Vorobjev, Y.N.; Zharkov, D.O.
Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase
BMC Struct. Biol.
17
005
2017
Lactococcus lactis (P42371), Lactococcus lactis
Manually annotated by BRENDA team