show all | hide all No of entries

Information on EC 3.2.2.21 - DNA-3-methyladenine glycosylase II and Organism(s) Escherichia coli and UniProt Accession P04395

for references in articles please use BRENDA:EC3.2.2.21
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.21 DNA-3-methyladenine glycosylase II
IUBMB Comments
Involved in the removal of alkylated bases from DNA in Escherichia coli (cf. EC 2.1.1.63 methylated-DNA---[protein]-cysteine S-methyltransferase).
Specify your search results
Select one or more organisms in this record: ?
This record set is specific for:
Escherichia coli
UNIPROT: P04395
Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
dna glycosylase, n-methylpurine-dna glycosylase, 3-methyladenine dna glycosylase ii, 3-methyladenine-dna glycosylase ii, alka protein, alkylpurine-dna-n-glycosylase, tagii, alka1, mag1 protein, helix-hairpin-helix dna glycosylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3-methyladenine DANN glycosylase II
294336
-
3-methyladenine DNA glycosylase II
246
-
3-methyladenine-DNA glycosidase II
-
-
-
0
3-methyladenine-DNA glycosylase II
-
-
-
0
AlkA protein
deoxyribonucleate 3-methyladenine glycosidase II
-
-
-
0
DNA-3-methyladenine glycosidase II
-
-
-
0
helix-hairpin-helix DNA glycosylase
294336
-
m3A DNA glycosylase II
246
-
TagII
-
-
-
0
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of N-glycosyl bond
-
-
-
0
SYSTEMATIC NAME
IUBMB Comments
alkylated-DNA glycohydrolase (releasing methyladenine and methylguanine)
Involved in the removal of alkylated bases from DNA in Escherichia coli (cf. EC 2.1.1.63 methylated-DNA---[protein]-cysteine S-methyltransferase).
CAS REGISTRY NUMBER
COMMENTARY hide
89287-38-7
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,2-propanediol-DNA + H2O
?
show the reaction diagram
-
-
-
?
1,3-propanediol-DNA + H2O
?
show the reaction diagram
-
-
-
?
alkylated DNA + H2O
3-methyl-2'-deoxyadenosine + 3-deaza-3-methyl-2'-deoxyadenosine + DNA
show the reaction diagram
the sequences of the oligos used in the assay are 5'-CGATAGCATCCTYCCTTCTCTCCAT-3', where Y is the location of the lesion base, and 5'-ATGGAGAGAAGGZAGGATGCTATCG-3' for the complementary strand, where Z is the base opposite the lesion
-
-
?
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + O2-methylthymine + O2-methylcytosine + 1,N6-ethenoadenine + hypoxanthine + DNA
show the reaction diagram
-
-
-
?
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + O2-methylthymine + O2-methylcytosine + DNA
show the reaction diagram
alkylated DNA + H2O
3-methyladenine + ?
show the reaction diagram
-
-
-
?
alkylated DNA + H2O
7-methyladenine + 7-methylguanine + 3-methyladenine + 3-methylguanine + purine + 6-chloropurine + xanthine + DNA
show the reaction diagram
-
7-methylguanine is cleaved the most quickly
-
?
ethanol-DNA + H2O
?
show the reaction diagram
best substrate
-
-
?
ethylene glycol-DNA + H2O
?
show the reaction diagram
-
-
-
?
glycerol-DNA + H2O
?
show the reaction diagram
-
-
-
?
methanol-DNA + H2O
?
show the reaction diagram
-
-
-
?
propanol-DNA + H2O
?
show the reaction diagram
-
-
-
?
3-methyladenine residues in alkylated DNA + H2O
3-methyladenine + DNA
show the reaction diagram
-
-
-
-
?
7-methylguanine residues in alkylated DNA + H2O
7-methylguanine + DNA
show the reaction diagram
-
-
-
-
?
alkylated DNA + H2O
3-methyladenine + 3-methylguanine + 7-methylguanine + 7-methyladenine + ?
show the reaction diagram
-
AlkA has significant glycosylase activity towards each of the normal bases in DNA. AlkA binds nonspecifically to DNA and neither mismatches nor 7-methylguanine lesions are specifically recognized in the ground state
-
-
?
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + 7-methyladenine + DNA
show the reaction diagram
-
-
-
-
?
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + O2-methylthymine + O2-methylcytosine + DNA
show the reaction diagram
alkylated DNA, treated with N-methyl-N'-nitro-N-nitrosoguanidine + H2O
?
show the reaction diagram
-
-
-
-
?
DNA treated with beta-[3H]propiolactone + H2O
N1-(carboxyethyl)adenine + N7-(carboxymethyl)guanine
show the reaction diagram
-
-
-
-
?
duplex oligonucleotide substrate containing ethenoadenine and hypoxanthine + H2O
ethenoadenine + hypoxanthine + oligonucleotide
show the reaction diagram
-
-
-
-
?
synthetic oligosaccharide + H2O
?
show the reaction diagram
-
synthetic oligosaccharide containing a single ethano or etheno adduct (3,N4-ethanocytosine, 1,N6-ethanoadenine, 3,N4-ethenocytosine or 1,N6-ethenoadenine), 20fold lower excision activity towards 3,N4-ethanocytosine and 1,N6-ethanoadenine than that towards their structurally analogous 3,N4-ethenocytosine or 1,N6-ethenoadenine. The enzyme is capable of excising the ethano base paired with any of the four natural bases
-
-
?
additional information
?
-
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
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + O2-methylthymine + O2-methylcytosine + DNA
show the reaction diagram
DNA repair enzyme, inducible base excision repair pathway of DNA alkylation damage
-
-
?
alkylated DNA + H2O
3-methyladenine + ?
show the reaction diagram
-
-
-
?
alkylated DNA + H2O
7-methyladenine + 7-methylguanine + 3-methyladenine + 3-methylguanine + purine + 6-chloropurine + xanthine + DNA
show the reaction diagram
-
7-methylguanine is cleaved the most quickly
-
?
alkylated DNA + H2O
3-methyladenine + 7-methylguanine + O2-methylthymine + O2-methylcytosine + DNA
show the reaction diagram
additional information
?
-
-
the enzyme is induced in response to DNA alkylation, and it protects cells from alkylated nucleobases by catalyzing their excision
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2'-deoxy-2'-fluoro-7-methylguanosine
-
DNA containing 1-azaribose
-
-
abasic-containing DNA
-
potent inhibitor
-
apurinic-DNA
-
-
-
Double-stranded DNA
-
-
N-ethylmaleimide
Pyrrolidine-containing oligonucleotide
-
-
-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
N-methyl-N'-nitro-N-nitrosoguanidine
spermidine
-
stimulates activity
spermine
-
stimulates activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0000092
3-methyladenine residues in alkylated DNA
-
pH 8.0, 37°C, release of 3-methyladenine
-
0.000011
7-methylguanine residues in alkylated DNA
-
pH 8.0, 37°C, release of 7-methylguanine
-
0.00000014 - 0.00003
alkylated DNA
0.000031 - 0.000053
alkylated DNA, treated with N-methyl-N'-nitro-N-nitrosoguanidine
-
0.042
duplex oligonucleotide substrate containing ethenoadenine and hypoxanthine
-
at 37°C, in 50 mM Na-MES buffer (pH 6.1)
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00125
duplex oligonucleotide substrate containing ethenoadenine and hypoxanthine
-
at 37°C, in 50 mM Na-MES buffer (pH 6.1)
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
30
duplex oligonucleotide substrate containing ethenoadenine and hypoxanthine
-
at 37°C, in 50 mM Na-MES buffer (pH 6.1)
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.3 - 7.4
-
isoelectric focusing
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
alkyladenine DNA glycosylase protects an abasic site on one strand of a DNA duplex from cross-linking with an amine on the opposing strand by binding tightly to the abasic site and sequestering it
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
27000
-
gel filtration
31000
-
SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
2.5 A crystal structure colmplexed to DNA, crystals belong to space group P3(1)21, cell dimensions a = B = 82.4 A and c = 199.7 A
AlkA in complex with undamaged DNA, sitting drop vapor diffusion method, using 25-29% (w/v) polyethylene glycol 3350, 100 mM bis-Tris, pH 6.0-6.6, 200 mM Li2S04, and 3% (w/v) 6-aminocaproic acid, at 25°C
crystal structure of AlkA solved with the multiple isomorphous replacement method, crystals grown with sitting-drop vapor-diffusion technique, space group P2(1), cell dimensions a = 58.61 A, b = 76.93 A, c = 62.27 A
-
hanging drop vapor difusion crystallization, space group P2(1), unit-cell parameters are a = 58.17, b = 76.27, c = 61.69, alpha = gamma = 90°, beta = 109.98°
-
sitting drop method of vapour diffusion, monoclinic space group C2, a = 58.6 A, b = 76.8 A, c = 62.2 A
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D238N
inactive
D238N
-
site-directed mutagenesis
W218A
-
site-directed mutagenesis
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
65 min time for 50% inactivation
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-70°C, purified enzyme remains stable for more than 4 years when stored in 20% glycerol,
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Mono Q column chromatography
Ni-NTA column chromatography and Source S cation exchange column chromatography
purified from an overproducing strain
-
purified from overproducing strains DH1 and HB101, harboring plasmid pYN3070
-
purified from strain JM105 harboring pAlk10 plasmid
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
alkAg+ gene cloned and sequenced
-
expressed in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
-
sulfur mustard, or mustard gas, bis-(2-chloroethyl)sulfide is carcinogenic to humans, acutely toxic to the skin, repiratory tract and eyes and causes a delayed bone marrow depression, knowledge of the DNA damage caused by this agent and the cellular defenses against this damage are of fundamental importance
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Evensen, G.; Seeberg, E.
Adaptation to alkylation resistance involves the induction of a DNA glycosylase
Nature
296
773-775
1982
Escherichia coli
Manually annotated by BRENDA team
Karran, P.; Hjelmgren, T.; Lindahl, T.
Induction of a DNA glycosylase for N-methylated purines is part of the adaptive response to alkylating agents
Nature
296
770-773
1982
Escherichia coli, no activity in Escherichia coli
Manually annotated by BRENDA team
Thomas, L.; Yang, C.H.; Goldthwait, D.A.
Two DNA glycosylases in Escherichia coli which release primarily 3-methyladenine
Biochemistry
21
1162-1169
1982
Escherichia coli, Escherichia coli BW 9062
Manually annotated by BRENDA team
Clarke, N.D.; Kvaal, M.; Seeberg, E.
Cloning of Escherichia coli genes encoding 3-methyladenine DNA glycosylases I and II
Mol. Gen. Genet.
197
368-372
1984
Escherichia coli
Manually annotated by BRENDA team
Riazuddin, S.; Athar, A.; Ahmed, Z.; Lali, S.M.; Sohail, A.
DNA glycosylase enzymes induced during chemical adaptation of M. luteus
Nucleic Acids Res.
15
6607-6624
1987
Escherichia coli, Micrococcus luteus
Manually annotated by BRENDA team
Bjelland, S.; Seeberg, E.
Different efficiencies of the Tag and AlkA DNA glycosylases from Escherichia coli in the removal of 3-methyladenine from single-stranded DNA
FEBS Lett.
397
127-129
1996
Escherichia coli
Manually annotated by BRENDA team
Yamagata, Y.; Odawara, K.; Tomita, K.; Nakabeppu, Y.; Sekiguchi, M.
Crystallization and preliminary X-ray diffraction studies of 3-methyladenine-DNA glycosylase II from Escherichia coli
J. Mol. Biol.
204
1055-1056
1988
Escherichia coli
Manually annotated by BRENDA team
Bjelland, S.; Birkeland, N.K.; Benneche, T.; Volden, G.; Seeberg, E.
DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the AlkA enzyme in Escherichia coli
J. Biol. Chem.
269
30489-30495
1994
Escherichia coli
Manually annotated by BRENDA team
Schaerer, O.D.; Ortholand, J.Y.; Ganesan, A.; Ezaz-Nikpay, K.; Verdine, G.L.
Specific binding of the DNA repair enzyme AlkA to a pyrrolidine-based inhibitor
J. Am. Chem. Soc.
117
6623-6624
1995
Escherichia coli
-
Manually annotated by BRENDA team
Matijasevic, Z.; Stering, A.; Niu, T.Q.; Austin-Ritchie, P.; Ludlum, D.B.
Release of sulfur mustard-modified DNA bases by Escherichia coli 3-methyladenine DNA glycosylase II
Carcinogenesis
17
2249-2252
1996
Escherichia coli
Manually annotated by BRENDA team
Yamagata, Y.; Kato, M.; Odawara, K.; Tokuno, Y.; Nakashima, Y.; Matsushima, N.; Yasumura, K.; Tomita, K.; Ihara, K.; Fujii, Y.; Nakabeppu, Y.; Sekiguchi, M.; Fujii, S.
Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli
Cell
86
311-319
1996
Escherichia coli
Manually annotated by BRENDA team
Borys, E.; Kusmierek, J.T.
Endogenous and exogenous DNA lesions recognized by N-alkylpurine-DNA glycosylases
Acta Biochim. Pol.
45
579-586
1998
Escherichia coli, Escherichia coli JM105
Manually annotated by BRENDA team
Je, K.H.; Son, J.K.; O'Connor, T.R.; Lee, C.S.
Hepsulfam induced DNA adducts and its excision repair by bacterial and mammalian 3-methyladenine DNA glycosylases
Mol. Cells
8
691-697
1998
Escherichia coli, Homo sapiens, Rattus norvegicus
Manually annotated by BRENDA team
Masaoka, A.; Terato, H.; Kobayashi, M.; Honsho, A.; Ohyama, Y.; Ide, H.
Enzymatic repair of 5-formyluracil. I. Excision of 5-formyluracil site-specifically incorporated into oligonucleotide substrates by alka protein (Escherichia coli 3-methyladenine DNA glycosylase II)
J. Biol. Chem.
274
25136-25143
1999
Escherichia coli, Escherichia coli MV1161
Manually annotated by BRENDA team
Terato, H.; Masaoka, A.; Kobayashi, M.; Fukushima, S.; Ohyama, Y.; Yoshida, M.; Ide, H.
Enzymatic repair of 5-formyluracil. II. Mismatch formation between 5-formyluracil and guanine during dna replication and its recognition by two proteins involved in base excision repair (AlkA) and mismatch repair (MutS)
J. Biol. Chem.
274
25144-25150
1999
Escherichia coli, Escherichia coli AB1157
Manually annotated by BRENDA team
Wyatt, M.D.; Allan, J.M.; Lau, A.Y.; Ellenberger, T.E.; Samson, L.D.
3-Methyladenine DNA glycosylases: structure, function, and biological importance
Bioessays
21
668-676
1999
Arabidopsis thaliana, Saccharomyces cerevisiae, Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe
Manually annotated by BRENDA team
Hollis, T.; Ichikawa, Y.; Ellenberger, T.
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA
EMBO J.
19
758-766
2000
Escherichia coli (P04395), Escherichia coli
Manually annotated by BRENDA team
Birkeland, N.K.; Anensen, H.; Knaevelsrud, I.; Kristoffersen, W.; Bjoras, M.; Robb, F.T.; Klungland, A.; Bjelland, S.
Methylpurine DNA glycosylase of the hyperthermophilic archaeon Archaeoglobus fulgidus
Biochemistry
41
12697-12705
2002
Archaeoglobus fulgidus, Escherichia coli
Manually annotated by BRENDA team
Teale, M.; Symersky, J.; DeLucas, L.
3-Methyladenine-DNA glycosylase II: the crystal structure of an AlkA-hypoxanthine complex suggests the possibility of product inhibition
Bioconjug. Chem.
13
403-407
2002
Escherichia coli
Manually annotated by BRENDA team
Terato, H.; Masaoka, A.; Asagoshi, K.; Honsho, A.; Ohyama, Y.; Suzuki, T.; Yamada, M.; Makino, K.; Yamamoto, K.; Ide, H.
Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid
Nucleic Acids Res.
30
4975-4984
2002
Escherichia coli, Escherichia coli MV1161
Manually annotated by BRENDA team
Guliaev, A.B.; Singer, B.; Hang, B.
Chloroethylnitrosourea-derived ethano cytosine and adenine adducts are substrates for Escherichia coli glycosylases excising analogous etheno adducts
DNA Repair
3
1311-1321
2004
Escherichia coli
Manually annotated by BRENDA team
O'Brien, P.J.; Ellenberger, T.
The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site
J. Biol. Chem.
279
26876-26884
2004
Escherichia coli
Manually annotated by BRENDA team
Zhao, B.; OBrien, P.J.
Kinetic mechanism for the excision of hypoxanthine by Escherichia coli AlkA and evidence for binding to DNA ends
Biochemistry
50
4350-4359
2011
Escherichia coli
Manually annotated by BRENDA team
Bowman, B.R.; Lee, S.; Wang, S.; Verdine, G.L.
Structure of Escherichia coli AlkA in complex with undamaged DNA
J. Biol. Chem.
285
35783-35791
2010
Escherichia coli (P04395), Escherichia coli
Manually annotated by BRENDA team
Admiraal, S.; O'Brien, P.
DNA-N-glycosylases process novel O-glycosidic sites in DNA
Biochemistry
52
4066-4074
2013
Escherichia coli (P04395), Escherichia coli
Manually annotated by BRENDA team
Michelson, A.Z.; Chen, M.; Wang, K.; Lee, J.K.
Gas-phase studies of purine 3-methyladenine DNA glycosylase II (AlkA) substrates
J. Am. Chem. Soc.
134
9622-9633
2012
Escherichia coli (P04395)
Manually annotated by BRENDA team
Admiraal, S.J.; O'Brien, P.J.
Base excision repair enzymes protect abasic sites in duplex DNA from interstrand cross-links
Biochemistry
54
1849-1857
2015
Escherichia coli, Homo sapiens (P29372), Homo sapiens
Manually annotated by BRENDA team
Select items on the left to see more content.