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show all sequences of 1.1.3.48

The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis

Gattis, S.G.; Chung, H.S.; Trent, M.S.; Raetz, C.R.; J. Biol. Chem. 288, 9216-9225 (2013)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression in Escherichia coli; gene kdnB, encoded in the Kdo8N biosynthetic cluster, DNA and amino acid sequence determination and analysis, subcloning and expression in Escherichia coli strains EC100D and WBB06 at 25C, recombinant expression of the gene cluster for 8-amino-3,8-dideoxy-D-manno-octulosonic acid biosynthesis from Shewanella oneidensis in Escherichia coli results in lipid A containing 8-amino-3,8-dideoxy-D-manno-octulosonic acid, and in vitro assays confirm the enzymatic functionality converting 3-deoxy-D-manno-octulosonic acid to 8-amino-3,8-dideoxy-D-manno-octulosonic acid, with incorporation into the Kdo8N-lipid A domain of LPS by a metal-dependent oxidase followed by a glutamate-dependent aminotransferase, recombinant expression of His-tagged enzyme in Escherichia coi strain C41
Shewanella oneidensis
Engineering
Amino acid exchange
Commentary
Organism
additional information
enzyme knockout by in-frame deletion, chromosomal deletion of kdnA/kdnB, overview. The knock-out strain shows increased sensitivity to polymyxin B (3fold) and bile salts (2fold)
Shewanella oneidensis
Inhibitors
Inhibitors
Commentary
Organism
Structure
EDTA
;
Shewanella oneidensis
additional information
no inhibition by NADH
Shewanella oneidensis
NAD+
slight inhibition
Shewanella oneidensis
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
activates, KdnB contains 0.51 mol of iron/mol of enzyme; or Mn2+, required
Shewanella oneidensis
Mn2+
activates, required for activity; or Fe2+, required
Shewanella oneidensis
additional information
KdnB is a metal-dependent enzyme
Shewanella oneidensis
Zn2+
KdnB contains 0.24 mol of iron/mol of enzyme
Shewanella oneidensis
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3-deoxy-alpha-D-manno-octulopyranosonate + O2
Shewanella oneidensis
-
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
Shewanella oneidensis MR-1 / ATCC 700550
-
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
Shewanella oneidensis
i.e. Kdo
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
Shewanella oneidensis MR-1 / ATCC 700550
i.e. Kdo
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Shewanella oneidensis
-
-
-
Shewanella oneidensis MR-1 / ATCC 700550
-
-
-
Shewanella oneidensis
Q8EEB0
gene kdnB or SO_2477
-
Shewanella oneidensis MR-1 / ATCC 700550
Q8EEB0
gene kdnB or SO_2477
-
Purification (Commentary)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coi strain C41 by nickel affinity chromatography, dialysis, and gel filtration, to homogeneity
Shewanella oneidensis
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3-deoxy-alpha-D-manno-octulopyranosonate + O2
-
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
-
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
-
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
-
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo, direct conversion of Kdo to 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) prior to its incorporation into the Kdo8N-lipid A domain of lipopolysaccharide by a metal-dependent oxidase KdnB followed by a glutamate-dependent aminotransferase KdnA, EC 2.3.1.09, the electron acceptor is molecular oxygen
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo, direct conversion of Kdo to 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) prior to its incorporation into the Kdo8N-lipid A domain of lipopolysaccharide by a metal-dependent oxidase KdnB followed by a glutamate-dependent aminotransferase KdnA, EC 2.3.1.09, the electron acceptor is molecular oxygen
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
additional information
the reaction catalyzed by KdnB is thermodynamically unfavorable and requires the second reaction catalyzed by KdnA to drive product formation, both enzymes are required for product formation. Enzyme KdnB appears to be an alcohol oxidase as opposed to an alcohol dehydrogenase, production of H2O2 when Mn-KdnB and PLP-KdnA, EC 2.6.1.109, are incubated with Kdo and L-Glu
734255
Shewanella oneidensis
?
-
-
-
-
additional information
the reaction catalyzed by KdnB is thermodynamically unfavorable and requires the second reaction catalyzed by KdnA to drive product formation, both enzymes are required for product formation. Enzyme KdnB appears to be an alcohol oxidase as opposed to an alcohol dehydrogenase, production of H2O2 when Mn-KdnB and PLP-KdnA, EC 2.6.1.109, are incubated with Kdo and L-Glu
734255
Shewanella oneidensis MR-1 / ATCC 700550
?
-
-
-
-
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
25
-
assay at
Shewanella oneidensis
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Shewanella oneidensis
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
NAD+ and NADP+ are not required for activity; NAD(P) is not required, and no product inhibition is observed for NADH
Shewanella oneidensis
Cloned(Commentary) (protein specific)
Commentary
Organism
expression in Escherichia coli
Shewanella oneidensis
gene kdnB, encoded in the Kdo8N biosynthetic cluster, DNA and amino acid sequence determination and analysis, subcloning and expression in Escherichia coli strains EC100D and WBB06 at 25C, recombinant expression of the gene cluster for 8-amino-3,8-dideoxy-D-manno-octulosonic acid biosynthesis from Shewanella oneidensis in Escherichia coli results in lipid A containing 8-amino-3,8-dideoxy-D-manno-octulosonic acid, and in vitro assays confirm the enzymatic functionality converting 3-deoxy-D-manno-octulosonic acid to 8-amino-3,8-dideoxy-D-manno-octulosonic acid, with incorporation into the Kdo8N-lipid A domain of LPS by a metal-dependent oxidase followed by a glutamate-dependent aminotransferase, recombinant expression of His-tagged enzyme in Escherichia coi strain C41
Shewanella oneidensis
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
NAD(P) is not required, and no product inhibition is observed for NADH
Shewanella oneidensis
additional information
NAD+ and NADP+ are not required for activity
Shewanella oneidensis
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
additional information
enzyme knockout by in-frame deletion, chromosomal deletion of kdnA/kdnB, overview. The knock-out strain shows increased sensitivity to polymyxin B (3fold) and bile salts (2fold)
Shewanella oneidensis
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
EDTA
-
Shewanella oneidensis
additional information
no inhibition by NADH
Shewanella oneidensis
NAD+
slight inhibition
Shewanella oneidensis
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
or Mn2+, required
Shewanella oneidensis
Fe2+
activates, KdnB contains 0.51 mol of iron/mol of enzyme
Shewanella oneidensis
Mn2+
or Fe2+, required
Shewanella oneidensis
Mn2+
activates, required for activity
Shewanella oneidensis
additional information
KdnB is a metal-dependent enzyme
Shewanella oneidensis
Zn2+
KdnB contains 0.24 mol of iron/mol of enzyme
Shewanella oneidensis
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
3-deoxy-alpha-D-manno-octulopyranosonate + O2
Shewanella oneidensis
-
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
Shewanella oneidensis MR-1 / ATCC 700550
-
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
Shewanella oneidensis
i.e. Kdo
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
Shewanella oneidensis MR-1 / ATCC 700550
i.e. Kdo
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coi strain C41 by nickel affinity chromatography, dialysis, and gel filtration, to homogeneity
Shewanella oneidensis
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3-deoxy-alpha-D-manno-octulopyranosonate + O2
-
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
-
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
-
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
-
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
enzyme oxidizes an alcohol using a metal and molecular oxygen
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo, direct conversion of Kdo to 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) prior to its incorporation into the Kdo8N-lipid A domain of lipopolysaccharide by a metal-dependent oxidase KdnB followed by a glutamate-dependent aminotransferase KdnA, EC 2.3.1.09, the electron acceptor is molecular oxygen
734255
Shewanella oneidensis
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
i.e. Kdo, direct conversion of Kdo to 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) prior to its incorporation into the Kdo8N-lipid A domain of lipopolysaccharide by a metal-dependent oxidase KdnB followed by a glutamate-dependent aminotransferase KdnA, EC 2.3.1.09, the electron acceptor is molecular oxygen
734255
Shewanella oneidensis MR-1 / ATCC 700550
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
-
-
?
additional information
the reaction catalyzed by KdnB is thermodynamically unfavorable and requires the second reaction catalyzed by KdnA to drive product formation, both enzymes are required for product formation. Enzyme KdnB appears to be an alcohol oxidase as opposed to an alcohol dehydrogenase, production of H2O2 when Mn-KdnB and PLP-KdnA, EC 2.6.1.109, are incubated with Kdo and L-Glu
734255
Shewanella oneidensis
?
-
-
-
-
additional information
the reaction catalyzed by KdnB is thermodynamically unfavorable and requires the second reaction catalyzed by KdnA to drive product formation, both enzymes are required for product formation. Enzyme KdnB appears to be an alcohol oxidase as opposed to an alcohol dehydrogenase, production of H2O2 when Mn-KdnB and PLP-KdnA, EC 2.6.1.109, are incubated with Kdo and L-Glu
734255
Shewanella oneidensis MR-1 / ATCC 700550
?
-
-
-
-
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
25
-
assay at
Shewanella oneidensis
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Shewanella oneidensis
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to a putative distinct class of metal-dependent alcohol oxidases
Shewanella oneidensis
malfunction
creation of an Shewanella oneidensis kdnA/kdnB in-frame deletion strain shows increased sensitivity to the cationic antimicrobial peptide polymyxin as well as bile salts by 3fold and 2fold, respectively
Shewanella oneidensis
metabolism
8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) biosynthesis pathway, 8-dehydro-3-deoxy-D-manno-octulosonic acid is directly converted to Kdo8N followed by incorporation into lipid A, overview. The entire gene cluster is required for 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) biosynthesis
Shewanella oneidensis
physiological function
a KdnB knock-out strain shows 3fold increased sensitivity to polymyxin B and 2fold increased sensitivity to bile salts; endotoxin lipopolysaccharide is composed of a hydrophobic anchor, known as lipid A, an inner core oligosaccharide, and a repeating O-antigen polysaccharide. The first sugar bridging the hydrophobic lipid A and the polysaccharide domain is 3-deoxy-D-manno-octulosonic acid. Derivative 8-amino-3,8-dideoxy-Dmanno-octulosonic acid is found exclusively in marine bacteria of the genus Shewanella. Data are consistent with direct conversion of 3-deoxy-D-manno-octulosonic acid to 8-amino-3,8-dideoxy-D-manno-octulosonic acid prior to its incorporation into the 8-amino-3,8-dideoxy-D-manno-octulosonic acid-lipid A domain of lipopolysaccharide by a metal-dependent oxidase followed by a glutamate-dependent aminotransferase; the first sugar bridging the hydrophobic lipid A and the polysaccharide domain is 3-deoxy-D-manno-octulosonic acid (Kdo), and thus it is critically important for lipopolysaccharide biosynthesis
Shewanella oneidensis
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to a putative distinct class of metal-dependent alcohol oxidases
Shewanella oneidensis
malfunction
creation of an Shewanella oneidensis kdnA/kdnB in-frame deletion strain shows increased sensitivity to the cationic antimicrobial peptide polymyxin as well as bile salts by 3fold and 2fold, respectively
Shewanella oneidensis
metabolism
8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) biosynthesis pathway, 8-dehydro-3-deoxy-D-manno-octulosonic acid is directly converted to Kdo8N followed by incorporation into lipid A, overview. The entire gene cluster is required for 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) biosynthesis
Shewanella oneidensis
physiological function
a KdnB knock-out strain shows 3fold increased sensitivity to polymyxin B and 2fold increased sensitivity to bile salts; endotoxin lipopolysaccharide is composed of a hydrophobic anchor, known as lipid A, an inner core oligosaccharide, and a repeating O-antigen polysaccharide. The first sugar bridging the hydrophobic lipid A and the polysaccharide domain is 3-deoxy-D-manno-octulosonic acid. Derivative 8-amino-3,8-dideoxy-Dmanno-octulosonic acid is found exclusively in marine bacteria of the genus Shewanella. Data are consistent with direct conversion of 3-deoxy-D-manno-octulosonic acid to 8-amino-3,8-dideoxy-D-manno-octulosonic acid prior to its incorporation into the 8-amino-3,8-dideoxy-D-manno-octulosonic acid-lipid A domain of lipopolysaccharide by a metal-dependent oxidase followed by a glutamate-dependent aminotransferase
Shewanella oneidensis
physiological function
the first sugar bridging the hydrophobic lipid A and the polysaccharide domain is 3-deoxy-D-manno-octulosonic acid (Kdo), and thus it is critically important for lipopolysaccharide biosynthesis
Shewanella oneidensis
Other publictions for EC 1.1.3.48
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
737728
Zachman-Brockmeyer
Structures of KdnB and KdnA fr ...
Shewanella oneidensis, Shewanella oneidensis ATCC 700550
Biochemistry
55
4485-4494
2016
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734255
Gattis
The origin of 8-amino-3,8-dide ...
Shewanella oneidensis, Shewanella oneidensis MR-1 / ATCC 700550
J. Biol. Chem.
288
9216-9225
2013
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