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Information on EC 5.3.2.3 - TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose-forming)
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5.3.2.3 TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose-forming)IUBMB Comments
The enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus.
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Word Map
- 5.3.2.3
-
5,6-dihydroxyindole-2-carboxylic
- dopachrome
- melanoma
-
dhica
-
tautomerase
- tyrosinase
-
cloudman
-
melanocyte-specific
-
melanogenesis
- melanin
-
isomerization
-
tautomerization
- synthesis
The enzyme appears in viruses and cellular organisms
Reaction Schemes
Synonyms
tdp-4-keto-6-deoxy-d-glucose-3,4-ketoisomerase, ravim, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dTDP-6-deoxy-D-xylo-hexos-4-ulose 3,4-ketoisomerase
FdtA
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose = dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
KEGG
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SYSTEMATIC NAME
IUBMB Comments
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose:dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose isomerase
The enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus.
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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
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
?
-
-
no characterization of the product due to its low yield
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
dTDP-3-dehydro-6-deoxy-alpha-D-galactose
-
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
-
-
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
Acinetobacter baumannii RCH51
-
-
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The glycan chain of the S-layer protein of Aneurinibacillus thermoaerophilus L420-91T (DSM 10154) consists of D-rhamnose and 3-acetamido-3,6-dideoxy-D-galactose (D-Fucp3NAc). Thymidine diphosphate-activated (D-Fucp3NAc) serves as precursor for the assembly of structural polysaccharides in Gram-positive and Gram-negative organisms. The biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose (dTDP-D-Fucp3NAc) involves five enzymes. FdtA is involved in this pathway
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
the enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The activity of FdtA is monitored by a simultaneous incubation with dTDP-6-deoxy-D-xylohex-4-ulose with FdtB and the required cosubstrates. The resulting product, dTDP-D-Fucp3N, is detectable by HPLC analysis
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
Site-directed mutagenesis experiments, enzymatic assays, and X-ray crystallographic analyses suggest that His49 functions as an active site base
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
the enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
Site-directed mutagenesis experiments, enzymatic assays, and X-ray crystallographic analyses suggest that His49 functions as an active site base
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The glycan chain of the S-layer protein of Aneurinibacillus thermoaerophilus L420-91T (DSM 10154) consists of D-rhamnose and 3-acetamido-3,6-dideoxy-D-galactose (D-Fucp3NAc). Thymidine diphosphate-activated (D-Fucp3NAc) serves as precursor for the assembly of structural polysaccharides in Gram-positive and Gram-negative organisms. The biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose (dTDP-D-Fucp3NAc) involves five enzymes. FdtA is involved in this pathway
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The activity of FdtA is monitored by a simultaneous incubation with dTDP-6-deoxy-D-xylohex-4-ulose with FdtB and the required cosubstrates. The resulting product, dTDP-D-Fucp3N, is detectable by HPLC analysis
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
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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
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
-
-
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
Acinetobacter baumannii RCH51
-
-
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The glycan chain of the S-layer protein of Aneurinibacillus thermoaerophilus L420-91T (DSM 10154) consists of D-rhamnose and 3-acetamido-3,6-dideoxy-D-galactose (D-Fucp3NAc). Thymidine diphosphate-activated (D-Fucp3NAc) serves as precursor for the assembly of structural polysaccharides in Gram-positive and Gram-negative organisms. The biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose (dTDP-D-Fucp3NAc) involves five enzymes. FdtA is involved in this pathway
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
the enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
the enzyme is involved in the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose. Four moieties of alpha-D-rhamnose and two moities of 3-acetamido-3,6-dideoxy-alpha-D-galactose form the repeating unit of the glycan chain in the S-layer of the bacterium Aneurinibacillus thermoaerophilus
-
-
?
dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose
dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-4-ulose. The glycan chain of the S-layer protein of Aneurinibacillus thermoaerophilus L420-91T (DSM 10154) consists of D-rhamnose and 3-acetamido-3,6-dideoxy-D-galactose (D-Fucp3NAc). Thymidine diphosphate-activated (D-Fucp3NAc) serves as precursor for the assembly of structural polysaccharides in Gram-positive and Gram-negative organisms. The biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose (dTDP-D-Fucp3NAc) involves five enzymes. FdtA is involved in this pathway
i.e. dTDP-6-deoxy-D-xylo-hexopyranos-3-ulose
-
r
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Melanoma
Upregulation of mRNA for the melanocortin-1 receptor but not for melanogenic proteins in macrophage x melanoma fusion hybrids exhibiting increased melanogenic and metastatic potential.
Melanoma, Experimental
Upregulation of mRNA for the melanocortin-1 receptor but not for melanogenic proteins in macrophage x melanoma fusion hybrids exhibiting increased melanogenic and metastatic potential.
Neoplasms
Upregulation of mRNA for the melanocortin-1 receptor but not for melanogenic proteins in macrophage x melanoma fusion hybrids exhibiting increased melanogenic and metastatic potential.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.045
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme H95R, at pH 7.5 and 37°C
0.15
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme Y35F, at pH 7.5 and 37°C
0.37
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y/H95R, at pH 7.5 and 37°C
0.41
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y, at pH 7.5 and 37°C
0.5
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
wild type enzyme, at pH 7.5 and 37°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.18
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y/H95R, at pH 7.5 and 37°C
0.19
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y, at pH 7.5 and 37°C
1.23
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme H95R, at pH 7.5 and 37°C
3.3
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme Y35F, at pH 7.5 and 37°C
10.5
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
wild type enzyme, at pH 7.5 and 37°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.46
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y, at pH 7.5 and 37°C
0.49
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme R15Y/H95R, at pH 7.5 and 37°C
21
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
wild type enzyme, at pH 7.5 and 37°C
22
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme Y35F, at pH 7.5 and 37°C
27
dTDP-4-dehydro-6-deoxy-alpha-D-glucose
mutant enzyme H95R, at pH 7.5 and 37°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Show AA Sequence and Transmembrane Helices (201 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
formation of the FdtA dimer represents a classical example of domain swapping whereby beta-strands 2 and 3 from one subunit form part of a beta-sheet in the second subunit
dimer
-
formation of the FdtA dimer represents a classical example of domain swapping whereby beta-strands 2 and 3 from one subunit form part of a beta-sheet in the second subunit
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization of wild-type and selenomethionine-labeled FdtA, crystallization of the mutant proteins (H49N, H51N, H49N/H51N), hanging-drop method of vapor diffusion, crystallization trials are conducted at both 25°C and 4°C. Three-dimensional structure of this sugar isomerase complexed with dTDP and solved to 1.5 A resolution. Crystals belong to the space group P4(1)2(1)2 with unit cell dimensions of a = b = 62.7 A and c = 201.3 A and one dimer per asymmetric unit
hanging drop vapor diffusion method, using 20% poly(ethylene glycol) 8000, 200 mM NaCl, and 100 mM MOPS (pH 7.0)
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H95R
the mutant shows increased activity compared to the wild type enzyme
R15Y
the mutant shows reduced activity compared to the wild type enzyme
R15Y/H95R
the mutant shows reduced activity compared to the wild type enzyme
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
to increase the stability, the enzyme is concentrated by ultrafiltration before storage at 4°C or -20°C and supplemented with 50% glycerol
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, the concentrated enzyme preparations are stable at 4°C for several months with only a marginal decrease of enzyme activity
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
synthesis of TDP-D-ravidosamine, necessary for in vitro glycosylation assays. TDP-D-ravidosamine is the anticipated sugar donor substrate of RavGT (the glycosyltransferase that links D-ravidosamine to the polyketide derived backbone defuco-gilvocarcin V). Defuco-gilvocarcin V exhibits superior anticancer/antibacterial activities
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Pfoestl, A.; Hofinger, A.; Kosma, P.; Messner, P.
Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-galactose in Aneurinibacillus thermoaerophilus L420-91T
J. Biol. Chem.
278
26410-26417
2003
Aneurinibacillus thermoaerophilus (Q6T1W8), Aneurinibacillus thermoaerophilus L420-91T, DSM 10154 (Q6T1W8)
brenda
Davis, M.L.; Thoden, J.B.; Holden, H.M.
The X-ray structure of dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase
J. Biol. Chem.
282
19227-19236
2007
Aneurinibacillus thermoaerophilus (Q6T1W8), Aneurinibacillus thermoaerophilus L420-91T (Q6T1W8)
brenda
Kharel, M.K.; Lian, H.; Rohr, J.
Characterization of the TDP-D-ravidosamine biosynthetic pathway: one-pot enzymatic synthesis of TDP-D-ravidosamine from thymidine-5-phosphate and glucose-1-phosphate
Org. Biomol. Chem.
9
1799-1808
2011
Streptomyces ravidus
brenda
Thoden, J.; Vinogradov, E.; Gilbert, M.; Salinger, A.; Holden, H.
Bacterial sugar 3,4-ketoisomerases structural insight into product stereochemistry
Biochemistry
54
4495-4506
2015
Aneurinibacillus thermoaerophilus (Q6T1W8)
brenda
Kenyon, J.; Kasimova, A.; Shneider, M.; Shashkov, A.; Arbatsky, N.; Popova, A.; Miroshnikov, K.; Hall, R.; Knirel, Y.
The KL24 gene cluster and a genomic island encoding a Wzy polymerase contribute genes needed for synthesis of the K24 capsular polysaccharide by the multiply antibiotic resistant Acinetobacter baumannii isolate RCH51
Microbiology
163
355-363
2017
Acinetobacter baumannii, Acinetobacter baumannii RCH51
brenda
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