Literature summary for 5.3.1.6 extracted from

Yoon, R.Y.; Yeom, S.J.; Kim, H.J.; Oh, D.K.
Novel substrates of a ribose-5-phosphate isomerase from Clostridium thermocellum (2009), J. Biotechnol., 139, 26-32.

Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli ER2566 cells	Acetivibrio thermocellus
gene rpiB, expression in Escherichia coli strain ER2566	Acetivibrio thermocellus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	kinetics with aldose and ketose substrates, recombinant enzyme, overview	Acetivibrio thermocellus
0.015	-	D-ribulose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus
0.017	-	D-ribose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus
15	-	D-ribulose 5-phosphate	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
17	-	D-ribose 5-phosphate	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
34	-	D-ribulose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
37	-	L-talose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
44	-	D-ribose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
53	-	D-psicose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
98	-	L-allose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
106	-	D-allose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
125	-	L-tagatose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
173	-	L-ribose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
232	-	D-talose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
319	-	L-ribulose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
17000	-	2 * 17000, gel filtration	Acetivibrio thermocellus
34000	-	gel filtration	Acetivibrio thermocellus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
D-ribose 5-phosphate	Acetivibrio thermocellus	preferred substrate	D-ribulose 5-phosphate	-	r

Organism

Organism	UniProt	Comment	Textmining
Acetivibrio thermocellus	-	-	-
Acetivibrio thermocellus	-	RpiB; gene rpiB	-

Purification (Commentary)

Purification (Comment)	Organism
HisTrap HP column chromatography	Acetivibrio thermocellus
recombinant RpiB from Escherichia coli strain ER2566 by His affinity chromatography	Acetivibrio thermocellus

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
0.21	-	purified enzyme, using D-tagatose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
0.53	-	purified enzyme, using L-allose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
12	-	purified enzyme, using L-psicose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
50	-	purified enzyme, using D-talose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
272	-	purified enzyme, using L-ribose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
600	-	purified enzyme, using L-allose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
720	-	purified enzyme, using L-ribulose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
1037	-	purified enzyme, using D-psicose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
1037	-	purified recombinant enzyme, substrate D-psicose	Acetivibrio thermocellus
1352	-	purified enzyme, using D-allose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
1352	-	purified recombinant enzyme, substrate D-allose	Acetivibrio thermocellus
5374	-	purified enzyme, using D-ribulose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
5374	-	purified recombinant enzyme, substrate D-ribulose	Acetivibrio thermocellus
5800	-	purified enzyme, using D-ribose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
5800	-	purified recombinant enzyme, substrate D-ribose	Acetivibrio thermocellus
7363	-	purified enzyme, using L-talose as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
7363	-	purified recombinant enzyme, substrate L-talose	Acetivibrio thermocellus
19680	-	purified enzyme, using D-ribulose 5-phosphate as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
19680	-	purified recombinant enzyme, substrate D-ribulose 5-phosphate	Acetivibrio thermocellus
25690	-	purified enzyme, using D-ribose 5-phosphate as substrate, at 65°C and pH 7.5	Acetivibrio thermocellus
25690	-	purified recombinant enzyme, substrate D-ribose 5-phosphate	Acetivibrio thermocellus

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
D-allose	-	Acetivibrio thermocellus	D-psicose	-	r
D-ribose	-	Acetivibrio thermocellus	D-ribulose	38% conversion to D-ribose 5-phosphate yield after approximately 90 min	r
D-ribose	39% conversion yield after approximately 90 min	Acetivibrio thermocellus	D-ribulose	-	r
D-ribose 5-phosphate	-	Acetivibrio thermocellus	D-ribulose 5-phosphate	-	r
D-ribose 5-phosphate	preferred substrate	Acetivibrio thermocellus	D-ribulose 5-phosphate	-	r
D-ribose 5-phosphate	preferred substrate	Acetivibrio thermocellus	D-ribulose 5-phosphate	38% conversion to D-ribose 5-phosphate yield after approximately 90 min at 50°C	r
D-talose	-	Acetivibrio thermocellus	D-tagatose	-	r
L-allose	-	Acetivibrio thermocellus	L-psicose	-	r
L-ribose	-	Acetivibrio thermocellus	L-ribulose	-	r
L-talose	89% conversion yield after approximately 90 min	Acetivibrio thermocellus	L-tagatose	-	r
L-talose	the enzyme prefers the forward reaction, high activity, 89% conversion to L-tagatose yield after approximately 90 min at 50°C	Acetivibrio thermocellus	L-tagatose	-	r
additional information	RpiB also displays activity with L-talose, D-ribose, D-allose, L-allose, L-ribose, and D-talose in decreasing order. The enzyme shows specificity for aldose substrates possessing hydroxyl groups oriented in the same direction at the C2, C3, and C4 positions. The substrate specificity through substrate interactions with residues Tyr42, His98, and His9, which interact with the hydroxyl groups of C2, C3, and C4, respectively, oriented in the same direction, homology molecular modeling, overview	Acetivibrio thermocellus	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	2 * 17000, gel filtration	Acetivibrio thermocellus
More	homology modeling of RpiB, substrate binding structure, overview	Acetivibrio thermocellus

Synonyms

Synonyms	Comment	Organism
D-ribose-5-phosphate isomerase	-	Acetivibrio thermocellus
RpiB	-	Acetivibrio thermocellus

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
65	-	assay at	Acetivibrio thermocellus

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
17	-	L-ribulose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
119	-	D-talose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
322	-	L-ribose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
1506	-	L-allose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
1822	-	L-tagatose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
2347	-	D-psicose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
2682	-	D-allose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
9193	-	D-ribulose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
11880	-	D-ribose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
13420	-	L-talose	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
39530	-	D-ribulose 5-phosphate	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
39530	-	D-ribulose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus
52000	-	D-ribose 5-phosphate	in 50 mM Tris-HCl buffer (pH 7.5), at 65°C	Acetivibrio thermocellus
52000	-	D-ribose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Acetivibrio thermocellus

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
2589	-	D-ribulose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus
3029	-	D-ribose 5-phosphate	pH 7.5, 65°C, recombinant enzyme	Acetivibrio thermocellus