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Information on EC 3.2.2.23 - DNA-formamidopyrimidine glycosylase and Organism(s) Geobacillus stearothermophilus and UniProt Accession P84131

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EC Tree
     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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Geobacillus stearothermophilus
UNIPROT: P84131
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Word Map
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
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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formamidopyrimidine-DNA glycosyl hydrolase
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formamidopyrimidine-DNA glycosylase
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FPG
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Fpg protein
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glycosidase, deoxyribonucleate formamidopyrimidine
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MutM
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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 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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?
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 containing 8-oxoguanine residues + H2O
DNA + 8-oxoguanine
show the reaction diagram
best substrate
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?
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
Fpg selectively facilitates eversion of 8-oxoguanine by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
P84131_GEOSE
274
0
30689
TrEMBL
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PDB
SCOP
CATH
UNIPROT
ORGANISM
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
8-oxoguanine is bound via E77 in syn conformation. In mutant E77S, which reflects the sequence of the Escherichia coli enzyme, 8-oxoguanine is preferentially bound in the anti conformation
FPG catalytic residues are suitably aligned for both 7,8-dihydro-8-oxoguanine syn- and anti-conformers, with anti-7,8-dihydro-8-oxoguanine forming a Watson-Crick pair with cytosine being more favorably bound. In the mechanism, sugar-ring opening may precede nucleoside deglycosylation
molecular dynamics simulations based on 1R2Y crystallographic data of the mutant E3Q/DNA complex. Binding of 8-oxoguanine in syn conformation is about 2.7 kcal/mol lower in energy than anti conformation
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molecular dynamics study based on X-ray structure of enzyme bound to 8-oxoguanine-containing DNA. Presence of the damaged base influences the dynamics of the whole enzyme. Loop location is dependent on the presence and on the conformation of 8-oxoguanine in its binding site
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E77S
in wild-type, 8-oxoguanine is bound via E77 in syn conformation. In mutant E77S, which reflects the sequence of the Escherichia coli enzyme, 8-oxoguanine is preferentially bound in the anti conformation
E3Q
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crystallization data
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Song, K.; Hornak, V.; de Los Santos, C.; Grollman, A.P.; Simmerling, C.
Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase
Biochemistry
45
10886-10894
2006
Geobacillus stearothermophilus (P84131), Geobacillus stearothermophilus
Manually annotated by BRENDA team
Song, K.; Kelso, C.; de los Santos, C.; Grollman, A.P.; Simmerling, C.
Molecular simulations reveal a common binding mode for glycosylase binding of oxidatively damaged DNA lesions
J. Am. Chem. Soc.
129
14536-14537
2007
Geobacillus stearothermophilus
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
Sowlati-Hashjin, S.; Wetmore, S.D.
Structural insight into the discrimination between 8-oxoguanine glycosidic conformers by DNA repair rnzymes A molecular dynamics study of human oxoguanine glycosylase 1 and formamidopyrimidine-DNA glycosylase
Biochemistry
57
1144-1154
2018
Geobacillus stearothermophilus (P84131)
Manually annotated by BRENDA team
Li, H.; Endutkin, A.V.; Bergonzo, C.; Campbell, A.J.; de los Santos, C.; Grollman, A.; Zharkov, D.O.; Simmerling, C.
A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine-DNA glycosylase
Nucleic Acids Res.
44
683-694
2016
Escherichia coli (P05523), Geobacillus stearothermophilus (P84131)
Manually annotated by BRENDA team