Literature summary for 5.1.3.1 extracted from

Akana, J.; Fedorov, A.A.; Fedorov, E.; Novak, W.R.; Babbitt, P.C.; Almo, S.C.; Gerlt, J.A.
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily (2006), Biochemistry, 45, 2493-2503.

Activating Compound

Activating Compound	Comment	Organism	Structure
Zn2+	RPE is activated by Zn2+ which binds with a stoichiometry of one ion per polypeptide	Streptococcus pyogenes

Cloned(Commentary)

Cloned (Comment)	Organism
the gene encoding RPE is expressed in the Escherichia coli strain BL21 (DE3)	Streptococcus pyogenes

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystal structure of the RPE is solved at 1.8 A resolution in the presence of D-xylitol 5-phosphate, an inert analogue of the D-xylulose 5-phosphate substrate. This structure suggests that the 2,3-enediolate intermediate in the 1,1-proton transfer reaction is stabilized by bidentate coordination to the Zn2+ that also is liganded to His 34, Asp 36, His 67, and Asp 176, the carboxylate groups of the Asp residues are positioned also to function as the acid/base catalysts	Streptococcus pyogenes

Crystallization (Comment)

Organism

crystal structure of the RPE is solved at 1.8 A resolution in the presence of D-xylitol 5-phosphate, an inert analogue of the D-xylulose 5-phosphate substrate. This structure suggests that the 2,3-enediolate intermediate in the 1,1-proton transfer reaction is stabilized by bidentate coordination to the Zn2+ that also is liganded to His 34, Asp 36, His 67, and Asp 176, the carboxylate groups of the Asp residues are positioned also to function as the acid/base catalysts

Streptococcus pyogenes

Protein Variants

Protein Variants	Comment	Organism
D176A	no detectable activity, substrate= 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes
D36A	no detectable activity, substrate= 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes
H34A	mutant discloses decreased affinity for Zn2+, kcat = 200/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2	Streptococcus pyogenes
H67A	mutant discloses decreased affinity for Zn2+, kcat = 270/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2	Streptococcus pyogenes
additional information	H34A, D36A, H67A, and D176A mutants are constructed since these His and Asp residues are strictly conserved in all RPEs and are observed to coordinate Zn2+ in the reported structures of the RPE from rice	Streptococcus pyogenes

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.2	-	D-ribulose 5-phosphate	-	Streptococcus pyogenes

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	assay carried out at 10 mM Mg2+	Streptococcus pyogenes

Organism

Organism	UniProt	Comment	Textmining
Streptococcus pyogenes	Q9A1H8	-	-

Purification (Commentary)

Purification (Comment)	Organism
lysate is applied to a chelating sepharose fast flow column charged with Ni2+, the N-terminal His tag is removed by thrombin cleavage	Streptococcus pyogenes

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
D-Ribulose 5-phosphate	-	Streptococcus pyogenes	D-Xylulose 5-phosphate	-	?

Synonyms

Synonyms	Comment	Organism
D-ribulose 5-phosphate 3-epimerase	-	Streptococcus pyogenes
RPE	-	Streptococcus pyogenes

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
100	-	D-ribulose 5-phosphate	RPE metal-free, stoichiometry of Zn2+: 0.1 ion per polypeptide, substrate 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes
200	-	D-ribulose 5-phosphate	mutant H34A, + 10 micromol/l ZnCl2	Streptococcus pyogenes
270	-	D-ribulose 5-phosphate	mutant H67A, + 10 micromol/l ZnCl2	Streptococcus pyogenes
480	-	D-ribulose 5-phosphate	RPE as isolated, stoichiometry of Zn2+: 0.3 ion per polypeptide, substrate 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes
840	-	D-ribulose 5-phosphate	RPE as isolated + 0.5 mM ZnCl2 present in assay, stoichiometry of Zn2+: 0.9 ion per polypeptide, substrate 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes
870	-	D-ribulose 5-phosphate	RPE metal-free + 0.5 mM ZnCl2 present in assay, stoichiometry of Zn2+: 0.9 ion per polypeptide, substrate 10 mM D-ribulose 5-phosphate	Streptococcus pyogenes

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Streptococcus pyogenes