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Literature summary extracted from

  • Nango, E.; Kumasaka, T.; Hirayama, T.; Tanaka, N.; Eguchi, T.
    Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+ (2008), Proteins, 70, 517-527.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.2.3.124 purified free enzyme and enzyme in complex with substrate analogue inhibitor carbaglucose 6-phosphate, and with NAD+, and Co2+, hanging drop vapour diffusion method, mixing of 0.002 ml pf 4.2 mg/ml protein in 5 mM Tris-HCl, pH 7.7, and 0.2 mM CoCl2, with 0.002 ml of reservoir solution containing 40% w/v PEG 4000, 200 mM Li2SO4, and 100 mM Tris-HCl, pH 8.6, equilibration against 1 ml of reservoir solution, addition of 1 mM Co2+ and 1 mM inhibitor, 4°C, X-ray diffraction structure determination and analysis at 2.15-2.3 A resoltuion, heavy atom derivatization Niallia circulans

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.2.3.124 carbaglucose-6-phosphate a substrate analogue inhibitor, binding structure, overview. The inhibitor coordinates a cobalt ion in the active site Niallia circulans

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.2.3.124 Co2+ required Niallia circulans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.2.3.124 D-glucose 6-phosphate Niallia circulans multistep reaction 2-deoxy-L-scyllo-inosose + phosphate
-
 ?
4.2.3.124 D-glucose 6-phosphate Niallia circulans SANK72073 multistep reaction 2-deoxy-L-scyllo-inosose + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.2.3.124 Niallia circulans Q9S5E2 gene btrC
-
4.2.3.124 Niallia circulans SANK72073 Q9S5E2 gene btrC
-

Reaction

EC Number Reaction Comment Organism Reaction ID
4.2.3.124 D-glucose 6-phosphate = 2-deoxy-L-scyllo-inosose + phosphate reaction mechanism of the multistep reaction, stereochemistry of the phosphate elimination reaction, proceeding through syn-elimination assisted by Glu 243, and the cyclization, an aldol condensation that proceeds via a boat conformation, overview Niallia circulans
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.3.124 D-glucose 6-phosphate multistep reaction Niallia circulans 2-deoxy-L-scyllo-inosose + phosphate
-
 ?
4.2.3.124 D-glucose 6-phosphate multistep reaction Niallia circulans SANK72073 2-deoxy-L-scyllo-inosose + phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
4.2.3.124 dimer two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer are different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change Niallia circulans

Synonyms

EC Number Synonyms Comment Organism
4.2.3.124 btrC
-
 Niallia circulans
4.2.3.124 DOIS
-
 Niallia circulans

Cofactor

EC Number Cofactor Comment Organism Structure
4.2.3.124 NAD+ required, binding strutcure in presence of inhibitor carbaglucose 6-phosphate Niallia circulans

General Information

EC Number General Information Comment Organism
4.2.3.124 metabolism key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase, which catalyzes carbocycle formation from D-glucose 6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction Niallia circulans
4.2.3.124 additional information active site structure is located between the N-terminal and C-terminal domains. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer are different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. Comparison of active site between the native and complex BtrC, overview Niallia circulans