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Enzyme Nomenclature
Information on EC 1.1.3.48 - 3-deoxy-alpha-D-manno-octulosonate 8-oxidase
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1.1.3.48 3-deoxy-alpha-D-manno-octulosonate 8-oxidaseIUBMB Comments
The enzyme, characterized from the bacterium Shewanella oneidensis, is involved in the formation of 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 2.6.1.109, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
kdnB
kdnB
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3-deoxy-alpha-D-manno-octulopyranosonate + O2 = 3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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SYSTEMATIC NAME
IUBMB Comments
3-deoxy-alpha-D-manno-octulopyranosonate:oxygen 8-oxidoreductase
The enzyme, characterized from the bacterium Shewanella oneidensis, is involved in the formation of 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 2.6.1.109, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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enzyme oxidizes an alcohol using a metal and molecular oxygen
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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-
-
?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
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enzyme oxidizes an alcohol using a metal and molecular oxygen
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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enzyme oxidizes an alcohol using a metal and molecular oxygen
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2 + L-Glu
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
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enzyme oxidizes an alcohol using a metal and molecular oxygen
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?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
i.e. Kdo
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-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
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
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-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
i.e. Kdo
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-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
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
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?
additional information
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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
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-
?
additional information
?
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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
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?
additional information
?
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Shewanella oneidensis MR-1 / ATCC 700550
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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
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?
additional information
?
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Shewanella oneidensis MR-1 / ATCC 700550
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
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?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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enzyme oxidizes an alcohol using a metal and molecular oxygen
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
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-
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?
3-deoxy-alpha-D-manno-octulopyranosonate + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonate + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
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enzyme oxidizes an alcohol using a metal and molecular oxygen
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
i.e. Kdo
-
-
?
3-deoxy-alpha-D-manno-octulosonic acid + O2
3,8-dideoxy-8-oxo-alpha-D-manno-octulosonic acid + H2O2
Shewanella oneidensis MR-1 / ATCC 700550
i.e. Kdo
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-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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NAD(P) is not required, and no product inhibition is observed for NADH
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additional information
NAD(P) is not required, and no product inhibition is observed for NADH
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additional information
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NAD+ and NADP+ are not required for activity
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additional information
NAD+ and NADP+ are not required for activity
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additional information
the enzyme does not require NAD(P) for activity
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Mn2+
additional information
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Shewanella oneidensis MR-1 / ATCC 700550
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
evolution
the enzyme belongs to a putative distinct class of metal-dependent alcohol oxidases
evolution
Shewanella oneidensis MR-1 / ATCC 700550
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the enzyme belongs to a putative distinct class of metal-dependent alcohol oxidases
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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
malfunction
Shewanella oneidensis MR-1 / ATCC 700550
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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
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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
metabolism
Shewanella oneidensis MR-1 / ATCC 700550
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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
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physiological function
a KdnB knock-out strain shows 3fold increased sensitivity to polymyxin B and 2fold increased sensitivity to bile salts
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
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
physiological function
Shewanella oneidensis MR-1 / ATCC 700550
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a KdnB knock-out strain shows 3fold increased sensitivity to polymyxin B and 2fold increased sensitivity to bile salts
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physiological function
Shewanella oneidensis MR-1 / ATCC 700550
-
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
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physiological function
Shewanella oneidensis MR-1 / ATCC 700550
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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
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A644TUJ1_9ZZZZ
359
1
39430
TrEMBL
Mitochondrion (Reliability: 5)
A0A644ZI22_9ZZZZ
413
0
45311
TrEMBL
Mitochondrion (Reliability: 4)
A0A645G3C2_9ZZZZ
121
0
13006
TrEMBL
Mitochondrion (Reliability: 2)
A0A484HL05_9DELT
358
0
39732
TrEMBL
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 7-9% (w/v) poly(ethylene glycol) 8000, 100 mM homo-PIPES (pH 5.0), and 1.0 M tetramethylammonium chloride
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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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)
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)
additional information
Shewanella oneidensis MR-1 / ATCC 700550
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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)
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coi strain C41 by nickel affinity chromatography, dialysis, and gel filtration, to homogeneity
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
J. Biol. Chem.
288
9216-9225
2013
Shewanella oneidensis, Shewanella oneidensis (Q8EEB0), Shewanella oneidensis MR-1 / ATCC 700550, Shewanella oneidensis MR-1 / ATCC 700550 (Q8EEB0)
brenda
Zachman-Brockmeyer, T.R.; Thoden, J.B.; Holden, H.M.
Structures of KdnB and KdnA from Shewanella oneidensis: Key enzymes in the formation of 8-amino-3,8-dideoxy-D-manno-octulosonic acid
Biochemistry
55
4485-4494
2016
Shewanella oneidensis (Q8EEB0), Shewanella oneidensis ATCC 700550 (Q8EEB0)
brenda
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Release 2023.1 (January 2023)
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