L-ribose production from L-arabinose by using purified L-arabinose isomerase and mannose-6-phosphate isomerase from Geobacillus thermodenitrificans

Yeom, S.J.; Kim, N.H.; Park, C.S.; Oh, D.K.; Appl. Environ. Microbiol. 75, 6941-6943 (2009)

Data extracted from this reference:

Cloned(Commentary)

Commentary	Organism
kdsD and gutQ, API is encoded by the two paralogous genes, which may substitute for each other, expression of His-tagged KdsD in Escherichia coli strain BL21(DE3), subcloning in strain DH5alpha	Escherichia coli

Inhibitors

Inhibitors	Commentary	Organism	Structure
Zn2+	inhibits substrate binding by the enzyme in a reversible manner	Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
D-Arabinose 5-phosphate	Escherichia coli	-	D-Ribulose 5-phosphate	-	-	?

Organism

Organism	Primary Accession No. (UniProt)	Commentary	Textmining
Escherichia coli	-	API is encoded by two paralogous genes kdsD and gutQ, which may substitute for each other	-

Purification (Commentary)

Commentary	Organism
recombinant His-tagged KdsD from Escherichia coli strain Bl21(DE3) by nickel affinity chromatography	Escherichia coli

Substrates and Products (Substrate)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
3-deoxy-D-arabinose 5-phosphate	KdsD converts 3-deoxy-A5P to 3-deoxy-Ru5P, but the catalysis proceeds tenfold slower than for the natural substrate isomerization	701812	Escherichia coli	3-deoxy-D-glycero-pentulose 5-phosphate	-	-	-	?
4-deoxy-D-arabinose 5-phosphate	KdsD converts 4-deoxy-A5P to 4-deoxy-Ru5P, but the catalysis proceeds slower than for the natural substrate isomerization	701812	Escherichia coli	4-deoxy-D-glycero-pentulose 5-phosphate	-	-	-	?
D-Arabinose 5-phosphate	-	701812	Escherichia coli	D-Ribulose 5-phosphate	-	-	-	?
More	KdsD substrate specificity, overview	701812	Escherichia coli	?	-	-	-	-

Subunits

Subunits	Commentary	Organism
tetramer	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Commentary	Organism
37	-	assay at	Escherichia coli

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Commentary	Organism
7.3	-	assay at	Escherichia coli

Cloned(Commentary) (protein specific)

Commentary	Organism
kdsD and gutQ, API is encoded by the two paralogous genes, which may substitute for each other, expression of His-tagged KdsD in Escherichia coli strain BL21(DE3), subcloning in strain DH5alpha	Escherichia coli

Inhibitors (protein specific)

Inhibitors	Commentary	Organism	Structure
Zn2+	inhibits substrate binding by the enzyme in a reversible manner	Escherichia coli

Natural Substrates/ Products (Substrates) (protein specific)

Natural Substrates	Organism	Commentary (Nat. Sub.)	Natural Products	Commentary (Nat. Pro.)	Organism (Nat. Pro.)	Reversibility
D-Arabinose 5-phosphate	Escherichia coli	-	D-Ribulose 5-phosphate	-	-	?

Purification (Commentary) (protein specific)

Commentary	Organism
recombinant His-tagged KdsD from Escherichia coli strain Bl21(DE3) by nickel affinity chromatography	Escherichia coli

Substrates and Products (Substrate) (protein specific)

Substrates	Commentary Substrates	Literature (Substrates)	Organism	Products	Commentary (Products)	Literature (Products)	Organism (Products)	Reversibility
3-deoxy-D-arabinose 5-phosphate	KdsD converts 3-deoxy-A5P to 3-deoxy-Ru5P, but the catalysis proceeds tenfold slower than for the natural substrate isomerization	701812	Escherichia coli	3-deoxy-D-glycero-pentulose 5-phosphate	-	-	-	?
4-deoxy-D-arabinose 5-phosphate	KdsD converts 4-deoxy-A5P to 4-deoxy-Ru5P, but the catalysis proceeds slower than for the natural substrate isomerization	701812	Escherichia coli	4-deoxy-D-glycero-pentulose 5-phosphate	-	-	-	?
D-Arabinose 5-phosphate	-	701812	Escherichia coli	D-Ribulose 5-phosphate	-	-	-	?
More	KdsD substrate specificity, overview	701812	Escherichia coli	?	-	-	-	-

Subunits (protein specific)

Subunits	Commentary	Organism
tetramer	-	Escherichia coli

Temperature Optimum [°C] (protein specific)

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Commentary	Organism
37	-	assay at	Escherichia coli

pH Optimum (protein specific)

pH Optimum Minimum	pH Optimum Maximum	Commentary	Organism
7.3	-	assay at	Escherichia coli

See also following references to EC number 5.3.1.13 (sorted by year of publication):

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)
714430	Yep		Enediol mimics as inhibitors o ...	Francisella tularensis	Bioorg. Med. Chem. Lett.	21	2679-2682	2011	-	-	1	-	-	-	4	1	-	-	-	-	-	4	-	-	1	-	-	-	-	-	1	-	-	-	-	1	-	-	-	-	-	-	4	-	-	1	-	-	-	-	4	4	-	1	-	-	-	-	-	-	-	1	-	-	-	-	1	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-
715380	Mosberg		A unique arabinose 5-phosphate ...	Escherichia coli	J. Bacteriol.	193	2981-2988	2011	1	-	1	-	-	-	3	2	-	9	1	-	-	6	-	-	1	-	-	-	-	-	3	1	-	-	-	2	1	1	-	-	-	-	-	1	-	1	-	-	-	-	-	3	-	2	-	9	1	-	-	-	-	1	-	-	-	-	3	1	-	-	-	2	1	1	-	-	-	2	2	-	2	2
714743	Airoldi		Targeting bacterial membranes: ...	Escherichia coli	Chemistry	16	1897-1902	2010	-	-	1	-	-	-	1	-	-	-	-	1	-	2	-	-	1	-	-	-	-	-	4	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	1	-	-	-	-	-	1	-	-	-	1	-	-	-	-	4	-	-	-	-	-	-	-	-	-	-	1	1	-	-	-
716854	Gourlay		Probing the active site of the ...	Escherichia coli	Protein Sci.	19	2430-2439	2010	-	-	1	1	2	-	-	-	-	-	1	-	-	2	-	-	1	-	-	-	1	-	1	1	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	1	2	-	-	-	-	-	-	-	1	-	-	-	-	1	-	-	1	-	1	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-
701812	Yeom		L-ribose production from L-ara ...	Escherichia coli	Appl. Environ. Microbiol.	75	6941-6943	2009	-	-	1	-	-	-	1	-	-	-	-	1	-	1	-	-	1	-	-	-	-	-	4	1	1	-	-	-	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	1	-	-	-	-	-	1	-	-	-	1	-	-	-	-	4	1	1	-	-	-	1	-	-	-	-	-	-	-	-	-
671856	Meredith		Characterization of Escherichi ...	Escherichia coli	Biochem. J.	395	427-432	2006	1	-	1	-	-	-	4	6	1	5	3	-	-	3	-	-	1	1	-	-	1	1	3	1	-	-	-	-	3	1	-	-	-	-	-	1	-	1	-	-	-	-	-	4	-	6	1	5	3	-	-	-	-	1	-	-	1	1	3	1	-	-	-	-	3	1	-	-	-	-	-	-	-	-
676073	Tan		Yersinia pestis YrbH is a mult ...	Yersinia pestis	Mol. Microbiol.	61	861-870	2006	-	-	-	-	1	-	-	-	-	-	-	-	-	4	-	-	-	1	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
660993	D'Aniello		Cephalopod vision involves dic ...	Escherichia coli	Biochem. J.	386	331-340	2005	-	-	1	-	-	-	3	2	-	-	1	-	-	1	-	-	1	-	-	-	-	-	1	-	-	-	-	2	1	-	-	-	-	-	-	-	-	1	-	-	-	-	-	3	-	2	-	-	1	-	-	-	-	1	-	-	-	-	1	-	-	-	-	2	1	-	-	-	-	-	-	-	-	-
662042	Meredith		Identification of GutQ from Es ...	Escherichia coli	J. Bacteriol.	187	6936-6942	2005	1	-	1	-	-	-	1	2	-	1	1	1	-	3	-	-	1	-	-	-	-	-	2	1	-	-	-	2	1	-	-	-	-	-	-	1	-	1	-	-	-	-	-	1	-	2	-	1	1	1	-	-	-	1	-	-	-	-	2	1	-	-	-	2	1	-	-	-	-	-	-	-	-	-
652445	Meredith		Escherichia coli YrbH is a D-a ...	Escherichia coli	J. Biol. Chem.	278	32771-32777	2003	-	-	1	-	-	-	6	2	-	-	1	1	-	3	-	-	1	-	-	-	1	1	3	1	-	-	-	2	1	1	-	-	-	-	1	-	-	1	-	-	-	-	1	6	-	2	-	-	1	1	-	-	-	1	-	-	1	1	3	1	-	-	-	2	1	1	-	-	-	-	-	-	-	-
645237	Tzeng		KpsF is the arabinose-5-phosph ...	Neisseria meningitidis	J. Biol. Chem.	277	24103-24113	2002	-	-	1	-	-	-	-	-	2	-	-	1	-	4	-	-	1	-	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	1	-	-	-	-	-	-	-	-	2	-	-	1	-	-	-	1	-	-	-	-	1	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
2625	Bigham		Inhibition of arabinose 5-phos ...	Escherichia coli	J. Med. Chem.	27	717-726	1984	-	-	-	-	-	-	2	2	-	-	1	1	-	2	-	-	-	1	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	2	-	2	-	-	1	1	-	-	-	-	-	-	-	-	2	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
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