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Literature summary for 1.1.3.48 extracted from

  • Gattis, S.G.; Chung, H.S.; Trent, M.S.; Raetz, C.R.
    The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis (2013), J. Biol. Chem., 288, 9216-9225.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) 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 25°C, 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

Protein Variants

Protein Variants Comment 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 Comment Organism Structure
EDTA
-
Shewanella oneidensis
additional information no inhibition by NADH Shewanella oneidensis
NAD+ slight inhibition Shewanella oneidensis

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ or Mn2+, required Shewanella oneidensis
Fe2+ activates, KdnB contains 0.51 mol of iron/mol of enzyme Shewanella oneidensis
Mn2+ activates, required for activity Shewanella oneidensis
Mn2+ 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 Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 UniProt Comment Textmining
Shewanella oneidensis
-
-
-
Shewanella oneidensis Q8EEB0 gene kdnB or SO_2477
-
Shewanella oneidensis MR-1 / ATCC 700550
-
-
-
Shewanella oneidensis MR-1 / ATCC 700550 Q8EEB0 gene kdnB or SO_2477
-

Purification (Commentary)

Purification (Comment) 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 Comment Substrates Organism Products Comment (Products) Rev. Reac.
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-octulopyranosonate + O2 + L-Glu
-
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
-
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 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 Shewanella oneidensis 3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2 i.e. Kdo 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 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 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 Shewanella oneidensis MR-1 / ATCC 700550 ?
-
?

Synonyms

Synonyms Comment Organism
kdnB
-
Shewanella oneidensis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Shewanella oneidensis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Shewanella oneidensis

Cofactor

Cofactor Comment 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

General Information

General Information Comment 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 Shewanella oneidensis
physiological function 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