BRENDA - Enzyme Database

Structure of the Escherichia coli heptosyltransferase WaaC: binary complexes with ADP and ADP-2-deoxy-2-fluoro heptose

Grizot, S.; Salem, M.; Vongsouthi, V.; Durand, L.; Moreau, F.; Dohi, H.; Vincent, S.; Escaich, S.; Ducruix, A.; J. Mol. Biol. 363, 383-394 (2006)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
2.4.99.B6
medicine
absence of the enzyme results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria. Thus, the enzyme represents a promising target in antibacterial drug design
Escherichia coli
Crystallization (Commentary)
EC Number
Crystallization
Organism
2.4.99.B6
crystals of the enzyme are grown at 18°C by the vapor-diffusion, hanging-drop method by mixing equal volumes of protein (4 mg/ml) and reservoir solution (100 mM Hepes (pH 7.0), 15% (w/v) PEG 1500, 100 mM NaCl (and 5 mM DTT in the case of the Se-Met protein)). Crystals grow within a few days as thin plates (0.15 mM x 0.15 mM x 0.050 mM) and belong to the orthorhombic space group P2(1)2(1)2(1) (a = 78 A, b = 88 A, c = 89 A) with two molecules in the asymmetric unit. Determination of the structure of the enzyme alone at 1.9 A resolution, and in complex with either ADP or the non-cleavable analog adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside (ADP-2-deoxy-2-fluoro-heptose) of the sugar donor at 2.4 A resolution. Both binary complexes offer a close view of the donor subsite and, together with results from site-directed mutagenesis studies, provide evidence for a model of the catalytic mechanism
Escherichia coli
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
2.4.99.B6
adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside
competitive inhibitor
Escherichia coli
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2.4.99.B6
ADP-L-glycero-beta-D-manno-heptose + (3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
Escherichia coli
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
ADP + alpha-L-glycero-D-manno-heptosyl-(1->5)-[(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)]-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
2.4.99.B6
Escherichia coli
P24173
pathogenic strain RS218
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.4.99.B6
ADP-L-glycero-beta-D-manno-heptose + (3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
728139
Escherichia coli
ADP + alpha-L-glycero-D-manno-heptosyl-(1->5)-[(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)]-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
2.4.99.B6
monomer
-
Escherichia coli
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.4.99.B6
7.5
-
assay at
Escherichia coli
IC50 Value
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
2.4.99.B6
0.03
-
pH 7.5, temperature not specified in the publication
Escherichia coli
adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside
Application (protein specific)
EC Number
Application
Commentary
Organism
2.4.99.B6
medicine
absence of the enzyme results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria. Thus, the enzyme represents a promising target in antibacterial drug design
Escherichia coli
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
2.4.99.B6
crystals of the enzyme are grown at 18°C by the vapor-diffusion, hanging-drop method by mixing equal volumes of protein (4 mg/ml) and reservoir solution (100 mM Hepes (pH 7.0), 15% (w/v) PEG 1500, 100 mM NaCl (and 5 mM DTT in the case of the Se-Met protein)). Crystals grow within a few days as thin plates (0.15 mM x 0.15 mM x 0.050 mM) and belong to the orthorhombic space group P2(1)2(1)2(1) (a = 78 A, b = 88 A, c = 89 A) with two molecules in the asymmetric unit. Determination of the structure of the enzyme alone at 1.9 A resolution, and in complex with either ADP or the non-cleavable analog adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside (ADP-2-deoxy-2-fluoro-heptose) of the sugar donor at 2.4 A resolution. Both binary complexes offer a close view of the donor subsite and, together with results from site-directed mutagenesis studies, provide evidence for a model of the catalytic mechanism
Escherichia coli
IC50 Value (protein specific)
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
2.4.99.B6
0.03
-
pH 7.5, temperature not specified in the publication
Escherichia coli
adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
2.4.99.B6
adenosine 5'-diphospho-2-deoxy-2-fluoro-L-glycero-beta-D-gluco-heptopyranoside
competitive inhibitor
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2.4.99.B6
ADP-L-glycero-beta-D-manno-heptose + (3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
Escherichia coli
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
ADP + alpha-L-glycero-D-manno-heptosyl-(1->5)-[(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)]-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
-
-
?
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.4.99.B6
ADP-L-glycero-beta-D-manno-heptose + (3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
728139
Escherichia coli
ADP + alpha-L-glycero-D-manno-heptosyl-(1->5)-[(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->4)]-(3-deoxy-alpha-D-manno-oct-2-ulopyranosylonate)-(2->6)-2-deoxy-2-[[(3R)-3-(dodecanoyloxy)tetradecanoyl]amino]-3-O-[(3R)-3-(tetradecanoyloxy)tetradecanoyl]-4-O-phospho-beta-D-glucopyranosyl-(1->6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[[(3R)-3-hydroxytetradecanoyl]amino]-1-O-phosphono-alpha-D-glucopyranose
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
2.4.99.B6
monomer
-
Escherichia coli
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.4.99.B6
7.5
-
assay at
Escherichia coli
General Information
EC Number
General Information
Commentary
Organism
2.4.99.B6
physiological function
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
Escherichia coli
General Information (protein specific)
EC Number
General Information
Commentary
Organism
2.4.99.B6
physiological function
the enzyme is involved in the synthesis of the inner core region of lipopolysaccharide. It catalyzes the addition of the first L-glycero-D-manno-heptose (heptose) molecule to one 3-deoxy-D-manno-oct-2-ulosonic acid residue of the Kdo2-lipid A molecule. Heptose is an essential component of the lipopolysaccharide core domain. Its absence results in a truncated lipopolysaccharide associated with the deeprough phenotype causing a greater susceptibility to antibiotic and an attenuated virulence for pathogenic Gram-negative bacteria
Escherichia coli