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Literature summary for 1.14.11.33 extracted from

  • Roy, T.W.; Bhagwat, A.S.
    Kinetic studies of Escherichia coli AlkB using a new fluorescence-based assay for DNA demethylation (2007), Nucleic Acids Res., 35, e147.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0034
-
single-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli
0.0054
-
single-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli
0.0062
-
double-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli
0.0093
-
double-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ required for activity, AlkB is a member of the non-heme iron (II) 2-oxoglutarate-dependent dioxygenase superfamily Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
DNA-1,N6-ethenoadenine + 2-oxoglutarate + O2 Escherichia coli
-
?
-
?
DNA-1-methylguanine + 2-oxoglutarate + O2 Escherichia coli
-
DNA-guanine + formaldehyde + succinate + CO2
-
?
DNA-3,N4-ethenocytosine + 2-oxoglutarate + O2 Escherichia coli
-
?
-
?
DNA-3-methylthymine + 2-oxoglutarate + O2 Escherichia coli
-
DNA-thymine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 Escherichia coli major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart DNA-adenine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 Escherichia coli major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart DNA-cytosine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 Escherichia coli major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart DNA-adenine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 Escherichia coli major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart DNA-cytosine + formaldehyde + succinate + CO2
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-

Purification (Commentary)

Purification (Comment) Organism
Ni-NTA column chromatography and SP-Sepharose cation exchange affinity column chromatography Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
DNA-1,N6-ethenoadenine + 2-oxoglutarate + O2
-
Escherichia coli ?
-
?
DNA-1-methylguanine + 2-oxoglutarate + O2
-
Escherichia coli DNA-guanine + formaldehyde + succinate + CO2
-
?
DNA-3,N4-ethenocytosine + 2-oxoglutarate + O2
-
Escherichia coli ?
-
?
DNA-3-methylthymine + 2-oxoglutarate + O2
-
Escherichia coli DNA-thymine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli DNA-adenine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli double-stranded DNA-adenine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli DNA-cytosine + formaldehyde + succinate + CO2
-
?
double-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli double-stranded DNA-cytosine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli DNA-adenine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-1-methyladenine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli single-stranded DNA-adenine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli DNA-cytosine + formaldehyde + succinate + CO2
-
?
single-stranded DNA-3-methylcytosine + 2-oxoglutarate + O2 major substrate, AlkB demethylates DNA-1-methyladenine and DNA-3-methylcytosine with comparable efficiencies and has only a modest preference for a single-stranded DNA substrate over its double-stranded DNA counterpart Escherichia coli single-stranded DNA-cytosine + formaldehyde + succinate + CO2
-
?

Synonyms

Synonyms Comment Organism
AlkB
-
Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.037
-
single-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli
0.052
-
double-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli
0.055
-
double-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli
0.062
-
single-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli

Cofactor

Cofactor Comment Organism Structure
2-oxoglutarate
-
Escherichia coli

General Information

General Information Comment Organism
physiological function the AlkB protein catalyzes the direct reversal of alkylation damage to DNA, primarily 1-methyladenine and 3-methylcytosine lesions created by endogenous or environmental alkylating agents Escherichia coli

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
5.8
-
double-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli
8
-
double-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli
10.8
-
single-stranded DNA-3-methylcytosine at 25°C, pH not specified in the publication Escherichia coli
11.3
-
single-stranded DNA-1-methyladenine at 25°C, pH not specified in the publication Escherichia coli