Literature summary for 3.5.1.108 extracted from

Hernick, M.; Gennadios, H.A.; Whittington, D.A.; Rusche, K.M.; Christianson, D.W.; Fierke, C.A.
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase functions through a general acid-base catalyst pair mechanism (2005), J. Biol. Chem., 280, 16969-16978.

Search for more literature for 3.5.1.108

Crystallization (Commentary)

Crystallization (Comment)	Organism
equilibrating a hanging drop containing 0.003 ml of protein solution (3 mg/ml LpxC, 100 mM HEPES, pH 7.5, 180 mM NaCl, 9-14% PEG3350, and 0.5 mM ZnSO4) and 0.003 ml of precipitant buffer (100 mM HEPES, pH 7.5, 180 mM NaCl, 9-14% PEG3350, and 0.5 mM ZnSO4) over a reservoir containing about 1 ml of precipitant buffer. Crystals with maximum dimensions of 0.3 * 0.15 * 0.15 mm3 grow within 3 days and are gradually transferred to a stabilization buffer of 100 mM sodium cacodylate, pH 6.0, 180 mM NaCl, 11-16% PEG 3350, 0.5 mM ZnSO4, and 1% glycerol. Crystals are flash-cooled in liquid nitrogen following cryoprotection with 22% glycerol and diffracted X-rays to 2.1 Å. Crystals are isomorphous with those prepared at pH 7.0 and belong to space group P6(1) with unit cell dimensions a = b = 101.3 A, c = 122.7 A	Aquifex aeolicus

Crystallization (Comment)

Organism

equilibrating a hanging drop containing 0.003 ml of protein solution (3 mg/ml LpxC, 100 mM HEPES, pH 7.5, 180 mM NaCl, 9-14% PEG3350, and 0.5 mM ZnSO4) and 0.003 ml of precipitant buffer (100 mM HEPES, pH 7.5, 180 mM NaCl, 9-14% PEG3350, and 0.5 mM ZnSO4) over a reservoir containing about 1 ml of precipitant buffer. Crystals with maximum dimensions of 0.3 * 0.15 * 0.15 mm3 grow within 3 days and are gradually transferred to a stabilization buffer of 100 mM sodium cacodylate, pH 6.0, 180 mM NaCl, 11-16% PEG 3350, 0.5 mM ZnSO4, and 1% glycerol. Crystals are flash-cooled in liquid nitrogen following cryoprotection with 22% glycerol and diffracted X-rays to 2.1 Å. Crystals are isomorphous with those prepared at pH 7.0 and belong to space group P6(1) with unit cell dimensions a = b = 101.3 A, c = 122.7 A

Aquifex aeolicus

Protein Variants

Protein Variants	Comment	Organism
D246A	1210fold decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Escherichia coli
D246A	decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Aquifex aeolicus
E78A	400fold decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Escherichia coli
E78A	decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Aquifex aeolicus
E78A/H265A	14800fold decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Escherichia coli
E78A/H265A	decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Aquifex aeolicus
H265A	2190fold decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Escherichia coli
H265A	decrease in kcat/KM compared to wild-type Zn2+-containing enzyme	Aquifex aeolicus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.00019	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type Zn2+-containing enzyme, steady-state	Escherichia coli
0.00025	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme D246A, steady-state	Escherichia coli
0.00047	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type enzyme substituted with Co2+, steady-state	Escherichia coli
0.0014	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme H265A, steady-state	Escherichia coli
0.0019	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A/H265A, steady-state	Escherichia coli
0.0043	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A, steady-state	Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Zn2+	zinc-dependent enzyme. LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile	Escherichia coli
Zn2+	zinc-dependent enzyme. LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile	Aquifex aeolicus

Organism

Organism	UniProt	Comment	Textmining
Aquifex aeolicus	O67848	-	-
Escherichia coli	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
-	Escherichia coli
-	Aquifex aeolicus

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine + H2O	LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile	Escherichia coli	UDP-3-O-((R)-3-hydroxymyristoyl)-D-glucosamine + acetate	-	?
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine + H2O	LpxC catalyzes deacetylation by using Glu78 and His265 as a general acid-base pair and the zinc-bound water as a nucleophile	Aquifex aeolicus	UDP-3-O-((R)-3-hydroxymyristoyl)-D-glucosamine + acetate	-	?

Synonyms

Synonyms	Comment	Organism
LpxC	-	Escherichia coli
LpxC	-	Aquifex aeolicus
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase	-	Escherichia coli
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase	-	Aquifex aeolicus

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Escherichia coli
30	-	assay at	Aquifex aeolicus

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.00096	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A/H265A, steady-state	Escherichia coli
0.0016	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme D246A, steady-state	Escherichia coli
0.005	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme H265A, steady-state	Escherichia coli
0.083	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A, steady-state	Escherichia coli
0.45	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type enzyme substituted with Co2+, steady-state	Escherichia coli
1.5	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type Zn2+-containing enzyme, steady-state	Escherichia coli

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Escherichia coli
7.5	-	assay at	Aquifex aeolicus

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
additional information	-	additional information	kcat/Km values are determined at 30°C and 60 °C, respectively, as a function of pH	Escherichia coli
additional information	-	additional information	kcat/Km values for deacetylation are determined at 30°C and 60°C, respectively, as a function of pH	Aquifex aeolicus
0.52	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A/H265A, steady-state	Escherichia coli
3.5	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme H265A, steady-state	Escherichia coli
6.3	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme D246A, steady-state	Escherichia coli
19.3	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, mutant enzyme E78A, steady-state	Escherichia coli
1083	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type enzyme substituted with Co2+, steady-state	Escherichia coli
7666	-	UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine	pH 7.5, 30°C, wild-type Zn2+-containing enzyme, steady-state	Escherichia coli