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2.5.1.78: 6,7-dimethyl-8-ribityllumazine synthase

This is an abbreviated version!
For detailed information about 6,7-dimethyl-8-ribityllumazine synthase, go to the full flat file.

Word Map on EC 2.5.1.78

Reaction

1-deoxy-L-glycero-tetrulose 4-phosphate
+
5-amino-6-(D-ribitylamino)uracil
=
6,7-dimethyl-8-(D-ribityl)lumazine
 + 2 H2O +
phosphate

Synonyms

6,7-dimethyl-8-(d-ribityl)lumazine synthase, 6,7-dimethyl-8-ribityllumazine synthase, 6,7-dimethyl-8-ribityllumazine synthase 1, 6,7-dimethyl-8-ribityllumazine synthase 2, 6,7-dimethyl-8-ribityllumazine-synthase, AaLS, BLS, DMRL synthase, DMRL synthase 2, heavy riboflavin synthase, LcLS1, LcLS2, lumazine synthase, lumazine synthase 1, lumazine synthase 2, lumazine synthase/riboflavin synthase complex, lumazinesynthase/riboflavin synthase complex, lumazinesynthase/riboflavin synthase complex, icosahedral capsid of 60 beta subunits enclosing a triplet of alpha subunits, luminazine synthase, MbtLS, MJ0303, Pbls, RIB4, ribE, RibH, ribH1, RibH1 protein, RibH2, type I lumazine synthase, type II lumazine synthase

ECTree

     2 Transferases
         2.5 Transferring alkyl or aryl groups, other than methyl groups
             2.5.1 Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)
                2.5.1.78 6,7-dimethyl-8-ribityllumazine synthase

Crystallization

Crystallization on EC 2.5.1.78 - 6,7-dimethyl-8-ribityllumazine synthase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallized at room temperature by sitting-drop vapor-diffusion method, the protein is crystallized in the cubic space group I23 with the cell dimensions a = b = c = 180.8 A, diffraction data are collected to 1.6 A resolution
-
sitting-drop vapor diffusion method, crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures are refined at resolutions of 1.72 A (enzyme-7-dioxo-5H-8-ribitylaminolumazine complex), 1.85 A (enzyme-3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid complex), 2.05 A (enzyme-5-nitroso-6-ribityl-amino-2,4(1H,3H)pyrimidinedione complex) and 2.2 A (enzyme-5-(6-D-ribitylamino-2,4(1H,3H)pyrimidinedione-5-yl)-1-pentyl-phosphonic acid complex), respectively. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single site mutants of lumazine synthase from Bacillus subtilis show that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, phosphate elimination, formation of the Schiff base and cyclization is proposed
-
substrate binding site structure analysis of Aquifex aeolicus lumazine synthase in complex with the inhibitor 3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid
to 3.5 A resolution. Structure reveals the icosahedral symmetry of the enzyme. Structure-based modeling of inhibitors 4-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-yl)-n-butyl 1-phosphate, 5-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-yl)-n-pentyl 1-phosphonate, 5-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-yl)-6-keton-hexyl 1-phosphate in the active site
-
crystal structure analysis of reconstituted, icosahedral beta-subunit capsids with bound substrate analogue inhibitor (5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione) at 2.4 A resolution
-
molecular modeling of enzyme with inhibitor 5-nitro-6-[[(2R,3R,4R)-2,3,4,5 tetrahydroxypentyl]sulfanyl]pyrimidine-2,4(1H,3H)-dione
-
molecular modeling of inhibitors to the active site
-
native protein, 2.4 A resolution, space group P6322 or C2. Mutant D44G/C93S/C139S/T118A crystallizes in space group R3 and diffracts to 1.6 A resolution
isoform RibH1, unliganded, to 2.2 A resolution, and bound to the substrate analogue inhibitor 5-nitro-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Comparison with structure of isoform RibH2
-
three-dimensional X-ray crystal structure of the enzyme solved and refined at 2.7 A resolution to a final R-value of 0.18. Structures of the enzyme from Bacillus subtilis and Bruvella abortus are compared
isoform RibH1, bound to the substrate analogue inhibitor 5-nitro-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. Comparison with structure of isoform RibH2
-
crystals are obtained by means of the hanging-drop, vapor-diffusion method at room temperature
-
crystallized in sitting drops by vapor diffusion. The crystal structure of lumazine synthase from Candida albicans is solved by molecular replacement and refined at 2.5 A resolution. The results of crystallographic investigations and sedimentation equilibrium experiments clearly indicate the presence of pentameric assemblies of the enzyme either in crystals or in solution
-
molecular modeling of enzyme in complex with inhibitor 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate. The pyrazolopyrimidinedione ring of the ligand is stacked with the indole ring of Trp27. The phosphate of the ligand is extensively hydrogen bonded with the one water molecule, the side chain nitrogens of Arg128, as well as the backbone nitrogens of Gln86 and Thr87 and the side-chain hydroxyl of Thr87. The ribityl hydroxyl groups are hydrogen bonded to the backbone nitrogen and oxygen of Asn114, the side-chain oxygens of Glu61, and the backbone nitrogen of Ile60. The pyrazolopyrimidinedione ring of the ligand is hydrogen bonded to the backbone nitrogen of Ala59, the backbone nitrogen of Ile83, backbone oxygen of Val81, and the side-chain nitrogen of Lys138
-
isoform RibH2, bound to the substrate analogue inhibitor 5-nitro-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
crystallized in the presence of two inhibitor compounds 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)propane 1-phosphate and 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrion-7-yl)butane 1-phosphate. The crystals are obtained in sitting drops by the vapor diffusion technique with the following macroseeding procedure
-
crystals are obtained in sitting drops by the vapour diffusion technique with the macroseeding procedure
-
in complex with inhibitor N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dion-5-ylpropionamide and phosphate, to 2.3 A resolution. The aromatic ring of the inhibitor is packed in the hydrophobic environment in the active site formed by Trp27, Ile60, Val81 and Val82, Ile83, Phe90, and Val93 residues of one subunit. The pyrimidine ring is in stacking interaction with the indole ring of Trp27 at a distance of 4 A
-
molecular modeling of binding of inhibitor 4-(6-chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl dihydrogen phosphate to luminazine synthase. The main forces stabilizing the complex with the enzyme involve pi-pi stacking interactions with Trp27 and hydrogen bonding of the phosphates with Arg128, the backbone nitrogens of Gly85 and Gln86, and the side chain hydroxyl of Thr87
-
molecular modeling of enzyme in complex with inhibitor 3-(1,3,7-trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)pentane 1-phosphate. The pyrazolopyrimidinedione ring of the ligand is stacked with the indole ring of Trp27. The phosphate of the ligand is extensively hydrogen bonded with the one water molecule, the side chain nitrogens of Arg128, as well as the backbone nitrogens of Gln86 and Thr87 and the side-chain hydroxyl of Thr87. The ribityl hydroxyl groups are hydrogen bonded to the backbone nitrogen and oxygen of Asn114, the side-chain oxygens of Glu61, and the backbone nitrogen of Ile60. The pyrazolopyrimidinedione ring of the ligand is hydrogen bonded to the backbone nitrogen of Ala59, the backbone nitrogen of Ile83, backbone oxygen of Val81, and the side-chain nitrogen of Lys138
-
sitting-drop vapour-diffusion method. Crystals of the recombinant enzyme with a size of up to 1.6 mm are obtained. The space group is P4(1)2(1)2 with lattice dimensions 82.9 A x 82.9 A x 300.2 A. X-ray diffraction data collected under cryogenic conditions are complete to 1.85 A resolution. The structure of the enzyme in complex with the intermediate analogue, 5-(6-D-ribitylamino-2,4-dihydroxypyrimidine-5-yl)-1-pentyl-phosphonic acid is solved via molecular replacement using the structure of the Bacillus subtilis enzyme as search model and is refined to a final R-factor of 19.8%
-
at 3.57 A resolution. Crystals belong to monoclinic space group P21, with 60 subunits per asymmetric unit, packed as an icosahedron. Enzyme contains an N-terminal proline residue
crystals are grown at 18°C by the sitting drop vapor diffusion method. The W27Y mutant protein in complex with riboflavin, the substrate analogue 5-nitroso-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, and the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine, are determined by X-ray crystallography at resolutions of 2.7–2.8 A
-
sitting drop vapour diffusion method, the enzyme is crystallised either in complex with bound riboflavin (RIBO) or in complex with the substrate analogue 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione (NRAP) or the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine (CEOL). The mutant proteins W27G, W63Y and W63Y/L119F, which do not bind riboflavin, and the mutant L119F, which only weakly binds to riboflavin, are also analysed. Diffraction data are collected to resolutions of 2.4 A (RIBO), 2.4 A (NRAP), 2.6 A (CEOL), 2.0 A (W27G), 3.1 A (W63Y and L119F) and 2.7 A (W63Y/L119F), respectively. All crystals belong to space group C222(1) with one pentamer in the asymmetric unit corresponding to the solution state of the protein
-
sitting-drop vapour diffusion method, crystallizes in space group C222(1). The crystals diffract to a resolution of 2.4 A
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 200 nl 8.4 mg/ml protein in 100 mM potassium phosphate, pH 7.5, and 150 mM NaCl, with 200 nl of reservoir solution containing 1.6 M ammonium sulfate, 100 mM sodium acetate pH 5.5, 100 mM sodium chloride, and equilibration against 0.1 ml reservoir solution, X-ray diffraction structure determination and analysis at 2.24 A resolution