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Literature summary extracted from

  • Yokoyama, K.; Numakura, M.; Kudo, F.; Ohmori, D.; Eguchi, T.
    Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin (2007), J. Am. Chem. Soc., 129, 15147-15155.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.99.38 expression in Escherichia coli Niallia circulans
1.3.98.3 expressed in Escherichia coli strain BL21(DE3) Niallia circulans

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.99.38 2-deoxy-scyllo-inosamine substrate inhibition Niallia circulans
1.3.98.3 2-deoxy-scyllo-inosamine uncompetitive substrate inhibition Niallia circulans
1.3.98.3 additional information not inhibited by S-adenosyl-L-methionine Niallia circulans

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.99.38 0.022
-
2-deoxy-scyllo-inosamine pH 8.0, 28°C Niallia circulans
1.1.99.38 0.46
-
S-adenosyl-L-methionine pH 8.0, 28°C Niallia circulans
1.3.98.3 0.022
-
2-deoxy-scyllo-inosamine in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C Niallia circulans
1.3.98.3 0.46
-
S-adenosyl-L-methionine apparent value, in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C Niallia circulans

Organism

EC Number Organism UniProt Comment Textmining
1.1.99.38 Niallia circulans Q8G907
-
-
1.3.98.3 Niallia circulans
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.3.98.3 His-bind resin column chromatography Niallia circulans

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.99.38 2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine enzyme catalyzes the oxidation of 2-deoxy-scyllo-inosamine under strictly anaerobic conditions along with consumption of an equimolar amount of S-adenosyl-L-methionine to produce 5-deoxyadenosine, methionine, and 3-amino-2,3-dideoxy-scylloinososeReaction follows the ordered Bi Ter mechanism and S-adenosyl-L-methionine is the first substrate and 2-deoxy-scyllo-inosamine is the second. The hydrogen atom at C-3 of 2-deoxy-scyllo-inosamine is directly transferred to 5-deoxyadenosine to give the radical intermediate of 2-deoxy-scyllo-inosamine in a reversible hydrogen abstraction step Niallia circulans 3-amino-2,3-dideoxy-scyllo-inosose + 5'-deoxyadenosine + L-methionine
-
?
1.1.99.38 2-deoxystreptamine + S-adenosyl-L-methionine 14.4% of the rate with 2-deoxy-scyllo-inosamine Niallia circulans ? + 5'-deoxyadenosine + L-methionine
-
?
1.1.99.38 additional information no substrates: 1D-chiro-inositol, 1L-chiro-inositol, muco-inositol, allo-inositol, D-glucose, D-glucosamine, D-xylose Niallia circulans ?
-
?
1.1.99.38 myo-inositol + S-adenosyl-L-methionine 0.9% of the rate with 2-deoxy-scyllo-inosamine Niallia circulans ? + 5'-deoxyadenosine + L-methionine
-
?
1.1.99.38 scyllo-inositol + S-adenosyl-L-methionine 3.3% of the rate with 2-deoxy-scyllo-inosamine Niallia circulans ? + 5'-deoxyadenosine + L-methionine
-
?
1.3.98.3 2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine 100% activity Niallia circulans 3-amino-2,3-dideoxy-scyllo-inosose + CO2 + L-methionine + 5'-deoxyadenosine
-
?
1.3.98.3 2-deoxystreptamine + S-adenosyl-L-methionine 14.4% activity compared to 2-deoxy-scyllo-inosamine Niallia circulans ? + CO2 + L-methionine + 5'-deoxyadenosine
-
?
1.3.98.3 additional information no activity with 1L-chiro-inositol, muco-inositol, allo-inositol, D-glucose, D-glucosamine, D-xylose, 1D-chiro-inositol, and 2,3-dideoxy-scyllo-inosose Niallia circulans ?
-
?
1.3.98.3 myo-inositol + S-adenosyl-L-methionine 0.9% activity compared to 2-deoxy-scyllo-inosamine Niallia circulans ? + CO2 + L-methionine + 5'-deoxyadenosine
-
?
1.3.98.3 scyllo-inositol + S-adenosyl-L-methionine 3.3% activity compared to 2-deoxy-scyllo-inosamine Niallia circulans ? + CO2 + L-methionine + 5'-deoxyadenosine
-
?

Synonyms

EC Number Synonyms Comment Organism
1.1.99.38 BtrN
-
Niallia circulans
1.3.98.3 BtrN BtrN is an unusual radical SAM dehydrogenase catalyzing the oxidation of the hydroxyl group by a radical mechanism Niallia circulans
1.3.98.3 oxygen-independent coproporphyrinogen-III oxidase
-
Niallia circulans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.99.38 0.02
-
S-adenosyl-L-methionine pH 8.0, 28°C Niallia circulans
1.1.99.38 0.033
-
2-deoxy-scyllo-inosamine pH 8.0, 28°C Niallia circulans
1.3.98.3 0.02
-
S-adenosyl-L-methionine apparent value, in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C Niallia circulans
1.3.98.3 0.038
-
2-deoxy-scyllo-inosamine in 50 mM HEPES-NaOH (pH 8.0) in the presence of 10 mM sodium dithionite at 28°C Niallia circulans

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.98.3 4Fe-4S-center
-
Niallia circulans

General Information

EC Number General Information Comment Organism
1.1.99.38 physiological function gene disruption causes the interruption of the biosynthetic pathway between 2-deoxy-scyllo-inosamine and 2-deoxystreptamine. In vitro assay of the overexpressed enzyme reveals that the enzyme catalyzes the oxidation of 2-deoxy-scyllo-inosamine under strictly anaerobic conditions along with consumption of an equimolar amount of S-adenosyl-L-methionine to produce 5-deoxyadenosine, methionine, and 3-amino-2,3-dideoxy-scyllo-inosose Niallia circulans