Literature summary for 5.3.1.5 extracted from

Toteva, M.M.; Silvaggi, N.R.; Allen, K.N.; Richard, J.P.
Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde (2011), Biochemistry, 50, 10170-10181.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
in complex with D-glyceraldehyde, hanging drop vapor diffusion method, using 0.2-0.3 M Mg-formate at pH 7.0 and 22°C	Streptomyces rubiginosus

Inhibitors

Inhibitors	Comment	Organism	Structure
D-glyceraldehyde	competitive inhibition of the isomerization of D-xylose	Streptomyces rubiginosus
D-Threonohydroxamic acid	competitive inhibitor, complete inhibition at 0.5 mM	Streptomyces rubiginosus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
3	-	D-glyceraldehyde	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus
4.9	-	D-xylose	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	used in assay conditions	Streptomyces rubiginosus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
D-Xylose	Streptomyces rubiginosus	-	D-Xylulose	-	r

Organism

Organism	UniProt	Comment	Textmining
Streptomyces rubiginosus	P24300	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
D-glyceraldehyde	-	Streptomyces rubiginosus	dihydroxyacetone	-	?
D-Xylose	-	Streptomyces rubiginosus	D-Xylulose	-	r

Synonyms

Synonyms	Comment	Organism
D-xylose isomerase	-	Streptomyces rubiginosus

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.0001	-	D-glyceraldehyde	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus
2.4	-	D-xylose	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.000034	-	D-glyceraldehyde	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus
0.49	-	D-xylose	in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25°C	Streptomyces rubiginosus

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Release 2023.1 (January 2023)