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Literature summary for 3.5.1.108 extracted from

  • Clayton, G.M.; Klein, D.J.; Rickert, K.W.; Patel, S.B.; Kornienko, M.; Zugay-Murphy, J.; Reid, J.C.; Tummala, S.; Sharma, S.; Singh, S.B.; Miesel, L.; Lumb, K.J.; Soisson, S.M.
    Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer (2013), J. Biol. Chem., 288, 34073-34080.
    View publication on PubMedView publication on EuropePMC

Application

Application Comment Organism
drug development the enzyme is a promising target for antibacterial drug development, structure-guided drug discovery of broad spectrum Gram-negative antibiotics Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
purified enzyme mutant C125S in complex with product UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine, hanging-drop vapor diffusion, mixing of 12 mg/ml protein in 20 mM HEPES, pH 7.0, 50 mM NaCl, and 0.5 mM zinc sulfate, with reservori solution containing 0.4 M NaH2PO4, 0.8 M K2HPO4, 0.2 M CAPS, pH 10.5, 50mM Li2SO4, 20°C, 3 days, X-ray diffraction structure determination and analysis at 2.59 A resolution, modeling Escherichia coli

Protein Variants

Protein Variants Comment Organism
C125S site-directed mutagenesis, crystal structure analysis Escherichia coli

Inhibitors

Inhibitors Comment Organism Structure
(2R)-N-hydroxy-2-[(naphthalene-2-sulfonyl)methyl]-3-(naphthalen-2-yl)propanamide
-
Escherichia coli
1,5-anhydro-2-deoxy-2-[(2Z)-2-hydroxy-2-(hydroxyimino)ethyl]-3-O-tetradecanoyl-L-mannitol
-
Escherichia coli
additional information structure-guided drug discovery of broad spectrum Gram-negative antibiotics, overview Escherichia coli
N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide
-
Escherichia coli
N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzamide
-
Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
additional information metal-dependent enzyme Escherichia coli
Zn2+ catalytic Zn2+ Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine + H2O Escherichia coli
-
UDP-3-O-[(3R)-3-hydroxymyristoyl]-alpha-D-glucosamine + acetate
-
r

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
gene lpxC
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information analysis of recognition of substrates and products by the enzyme, phosphate binding is stabilized by the catalytic Zn2+ and an extensive network of hydrogen bonds to key active site residues and myr-UDP-GlcN, overview Escherichia coli ?
-
?
UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine + H2O
-
Escherichia coli UDP-3-O-[(3R)-3-hydroxymyristoyl]-alpha-D-glucosamine + acetate
-
r
UDP-3-O-[(3R)-3-hydroxymyristoyl]-N-acetyl-alpha-D-glucosamine + H2O via tetrahedral transition state Escherichia coli UDP-3-O-[(3R)-3-hydroxymyristoyl]-alpha-D-glucosamine + acetate
-
r

Synonyms

Synonyms Comment Organism
LpxC
-
Escherichia coli

General Information

General Information Comment Organism
metabolism LpxC enzyme catalyzes the committed step of lipopolysaccharide biosynthesis Escherichia coli
physiological function LpxC is a metal-dependent deacetylase essential for lipopolysaccharide biosynthesis Escherichia coli