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Literature summary extracted from
- 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
| EC Number | Activating Compound | Comment | Organism | Structure |
|---|---|---|---|---|
| 5.1.3.1 | Zn2+ | RPE is activated by Zn2+ which binds with a stoichiometry of one ion per polypeptide | Streptococcus pyogenes |  |
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 5.1.3.1 | the gene encoding RPE is expressed in the Escherichia coli strain BL21 (DE3) | Streptococcus pyogenes |
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 4.1.1.85 | - |
Escherichia coli |
| 5.1.3.1 | 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
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 5.1.3.1 | D176A | no detectable activity, substrate= 10 mM D-ribulose 5-phosphate | Streptococcus pyogenes |
| 5.1.3.1 | D36A | no detectable activity, substrate= 10 mM D-ribulose 5-phosphate | Streptococcus pyogenes |
| 5.1.3.1 | H34A | mutant discloses decreased affinity for Zn2+, kcat = 200/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2 | Streptococcus pyogenes |
| 5.1.3.1 | H67A | mutant discloses decreased affinity for Zn2+, kcat = 270/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2 | Streptococcus pyogenes |
| 5.1.3.1 | 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]
| EC Number | KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.3.1 | 0.2 | - |
D-ribulose 5-phosphate | - |
Streptococcus pyogenes | |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 4.1.1.85 | Mg2+ | - |
Escherichia coli | |
| 5.1.3.1 | Mg2+ | assay carried out at 10 mM Mg2+ | Streptococcus pyogenes | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 4.1.1.85 | Escherichia coli | - |
- |
- |
| 5.1.3.1 | Streptococcus pyogenes | Q9A1H8 | - |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 5.1.3.1 | 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)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.1.1.85 | 3-dehydro-L-gulonate 6-phosphate + H+ | - |
Escherichia coli | L-xylulose 5-phosphate + CO2 | - |
? | |
| 5.1.3.1 | D-Ribulose 5-phosphate | - |
Streptococcus pyogenes | D-Xylulose 5-phosphate | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 4.1.1.85 | dimer | x-ray crystallography | Escherichia coli |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 4.1.1.85 | 3-keto-L-gulonate 6-phosphate decarboxylase | - |
Escherichia coli |
| 4.1.1.85 | KGPDC | - |
Escherichia coli |
| 5.1.3.1 | D-ribulose 5-phosphate 3-epimerase | - |
Streptococcus pyogenes |
| 5.1.3.1 | RPE | - |
Streptococcus pyogenes |
Turnover Number [1/s]
| EC Number | Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|---|
| 5.1.3.1 | 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 | |
| 5.1.3.1 | 200 | - |
D-ribulose 5-phosphate | mutant H34A, + 10 micromol/l ZnCl2 | Streptococcus pyogenes | |
| 5.1.3.1 | 270 | - |
D-ribulose 5-phosphate | mutant H67A, + 10 micromol/l ZnCl2 | Streptococcus pyogenes | |
| 5.1.3.1 | 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 | |
| 5.1.3.1 | 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 | |
| 5.1.3.1 | 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
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 5.1.3.1 | 7.5 | - |
assay at | Streptococcus pyogenes |
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