BRENDA - Enzyme Database

Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate

St Maurice, M.; Mera, P.; Park, K.; Brunold, T.C.; Escalante-Semerena, J.C.; Rayment, I.; Biochemistry 47, 5755-5766 (2008)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
2.5.1.17
medicine
ACA-mediated catalysis provides insights in molecular basis for dysfunction in methylmalonic aciduria
Lactobacillus reuteri
Crystallization (Commentary)
EC Number
Crystallization
Organism
2.5.1.17
trimer of three independent five-helix bundles, active sites at the interface between adjacent monomers, no significant structural changes accompany catalysis, precatalytic complex with ATP: cob(II)alamin (PDB: 3CI1, four-coordinate, base-off cob(II)alamin intermediate, enzyme with fully ordered six C-terminal residues and potassium ion in active site), complex with tripolyphosphate: adenosylcobalamin (PDB: 3CI3, partially occupied with five-coordinate adenosylcobalamin), precatalytic complex with ATP: cob(II)inamide (PDB: 3CI4, cob(II)inamide-binding structurally indistinguishable from cob(II)alamin-binding), binding of cobalamin and cobinamide (lacking dimethylbenzimidazole moiety) in identical positions and orientation, space group R3, one molecule in asymmetric unit, unit cell parameters: a: 67.8-68, b: 67.8-68, c: 110.9-111.3, beta: 90░, molecular replacement using PDB: 2NT8 as model; vapour-diffusion with tag-cleaved protein solution (18-22 mg/ml, in presence of hydroxycobalamin and/or adenosylcobalamin or dicyanocobinamide, ATP etc.) and reservoir solution (10-13% (w/v) PEG 8000, pH 6), cubic crystals, crystallisation under anoxic conditions in presence of flavin-dependent reducing system
Lactobacillus reuteri
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
2.5.1.17
cobinamide
substrate inhibition
Lactobacillus reuteri
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
2.5.1.17
Lactobacillus reuteri
-
-
-
Reaction
EC Number
Reaction
Commentary
Organism
2.5.1.17
2 ATP + 2 cob(II)yrinic acid a,c-diamide + a reduced flavoprotein = 2 triphosphate + 2 adenosylcob(III)yrinic acid a,c-diamide + an oxidized flavoprotein
not yet confimed
Lactobacillus reuteri
Specific Activity [micromol/min/mg]
EC Number
Specific Activity Minimum [Ámol/min/mg]
Specific Activity Maximum [Ámol/min/mg]
Commentary
Organism
2.5.1.17
0.0005
-
in presence of 1 mM ATP, 20 mM NADH, 2 mM FMN, 0.5 mM hydroxycobalamin and NAD(P)H: flavin oxidoreductase, 1.5 mM MgCl2, 100 mM KCl, pH 6
Lactobacillus reuteri
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.5.1.17
ATP + hydroxycobalamin
coenzyme B12 synthesis from vitamin B12, dimethylbenzimidazole arm of vitamin B12 plays no role in substrate positioning, corrinoid adenosylation assay: anaerobic, pH 6, 25░C, 1 or 2 mM FMN, 10 or 20 mM NADH, NAD(P)H: flavin oxidoreductase, 2 h incubation for complete reduction of hydroxycobalamin to cob(II)alamin before initiation of adenosyltransfer
690964
Lactobacillus reuteri
tripolyphosphate + adenosylcobalamin + H2O
measuring difference in absorbance by adenosylcobalamin at 525 nm
-
-
?
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.5.1.17
additional information
-
additional information
adenosylation of cobalamin and cobinamide (lacking dimethylbenzimidazole moiety) at similar rates
Lactobacillus reuteri
Application (protein specific)
EC Number
Application
Commentary
Organism
2.5.1.17
medicine
ACA-mediated catalysis provides insights in molecular basis for dysfunction in methylmalonic aciduria
Lactobacillus reuteri
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
2.5.1.17
trimer of three independent five-helix bundles, active sites at the interface between adjacent monomers, no significant structural changes accompany catalysis, precatalytic complex with ATP: cob(II)alamin (PDB: 3CI1, four-coordinate, base-off cob(II)alamin intermediate, enzyme with fully ordered six C-terminal residues and potassium ion in active site), complex with tripolyphosphate: adenosylcobalamin (PDB: 3CI3, partially occupied with five-coordinate adenosylcobalamin), precatalytic complex with ATP: cob(II)inamide (PDB: 3CI4, cob(II)inamide-binding structurally indistinguishable from cob(II)alamin-binding), binding of cobalamin and cobinamide (lacking dimethylbenzimidazole moiety) in identical positions and orientation, space group R3, one molecule in asymmetric unit, unit cell parameters: a: 67.8-68, b: 67.8-68, c: 110.9-111.3, beta: 90░, molecular replacement using PDB: 2NT8 as model; vapour-diffusion with tag-cleaved protein solution (18-22 mg/ml, in presence of hydroxycobalamin and/or adenosylcobalamin or dicyanocobinamide, ATP etc.) and reservoir solution (10-13% (w/v) PEG 8000, pH 6), cubic crystals, crystallisation under anoxic conditions in presence of flavin-dependent reducing system
Lactobacillus reuteri
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
2.5.1.17
cobinamide
substrate inhibition
Lactobacillus reuteri
Specific Activity [micromol/min/mg] (protein specific)
EC Number
Specific Activity Minimum [Ámol/min/mg]
Specific Activity Maximum [Ámol/min/mg]
Commentary
Organism
2.5.1.17
0.0005
-
in presence of 1 mM ATP, 20 mM NADH, 2 mM FMN, 0.5 mM hydroxycobalamin and NAD(P)H: flavin oxidoreductase, 1.5 mM MgCl2, 100 mM KCl, pH 6
Lactobacillus reuteri
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.5.1.17
ATP + hydroxycobalamin
coenzyme B12 synthesis from vitamin B12, dimethylbenzimidazole arm of vitamin B12 plays no role in substrate positioning, corrinoid adenosylation assay: anaerobic, pH 6, 25░C, 1 or 2 mM FMN, 10 or 20 mM NADH, NAD(P)H: flavin oxidoreductase, 2 h incubation for complete reduction of hydroxycobalamin to cob(II)alamin before initiation of adenosyltransfer
690964
Lactobacillus reuteri
tripolyphosphate + adenosylcobalamin + H2O
measuring difference in absorbance by adenosylcobalamin at 525 nm
-
-
?
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
2.5.1.17
additional information
-
additional information
adenosylation of cobalamin and cobinamide (lacking dimethylbenzimidazole moiety) at similar rates
Lactobacillus reuteri