Information on EC 5.1.3.1 - ribulose-phosphate 3-epimerase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
5.1.3.1
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RECOMMENDED NAME
GeneOntology No.
ribulose-phosphate 3-epimerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-ribulose 5-phosphate = D-xylulose 5-phosphate
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
epimerization
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Bifidobacterium shunt
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Biosynthesis of antibiotics
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Biosynthesis of secondary metabolites
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Calvin-Benson-Bassham cycle
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Carbon fixation in photosynthetic organisms
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formaldehyde assimilation II (RuMP Cycle)
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formaldehyde assimilation III (dihydroxyacetone cycle)
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heterolactic fermentation
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Metabolic pathways
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Microbial metabolism in diverse environments
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Pentose and glucuronate interconversions
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pentose phosphate pathway
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Pentose phosphate pathway
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pentose phosphate pathway (non-oxidative branch)
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pentose phosphate pathway (partial)
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photosynthesis
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Rubisco shunt
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SYSTEMATIC NAME
IUBMB Comments
D-ribulose-5-phosphate 3-epimerase
The enzyme also converts D-erythrose 4-phosphate into D-erythrulose 4-phosphate and D-threose 4-phosphate.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-20-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
mutant strain that lacks D-ribulose-5-phosphate 3-epimerase
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
basonym Alcaligenes eutrophus
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Pigeon
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-Ribulose 5-phosphate
D-Xylulose 5-phosphate
show the reaction diagram
D-xylulose 5-phosphate
D-ribulose 5-phosphate
show the reaction diagram
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?
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-Ribulose 5-phosphate
D-Xylulose 5-phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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Co2+ is able to activate the enzyme in vitro
Mg2+
assay carried out at 10 mM Mg2+
Mn2+
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manganese can activate the enzyme in vitro in place of iron converting the enzyme to a form that is unaffected by H2O2
Zn2+
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Zn2+ is able to activate the enzyme in vitro
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Cu(CH3COO)2
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D-deoxyribose 5-phosphate
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DL-alpha-glycerophosphate
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competitive
HgCl2
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iodoacetate
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weak
NEM
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weak
PCMB
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potassium phosphate
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weak
SO42-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Zn2+
RPE is activated by Zn2+ which binds with a stoichiometry of one ion per polypeptide
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.19 - 15
D-ribulose 5-phosphate
2.4 - 2.9
D-ribulose-5-phosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00033 - 7100
D-ribulose 5-phosphate
1300
D-xylulose 5-phosphate
Saccharomyces cerevisiae
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.9
DL-alpha-glycerophosphate
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25°C, pH 8.0
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4 - 7.6
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8.3
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; reaction with D-ribulose 5-phosphate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
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pH 6.5: about 90% of maximal activity, pH 9.0: 95% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.3 - 6.8
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wild-type enzyme and mutant enzyme D186E, denaturing isoelectric focusing, pH gradient 5-8
6.6
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mutant enzymes D186A and D186N, denaturing isoelectric focusing, pH gradient 5-8
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
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similar growth rates between the strains and identical soluble proteomes for wild-type and zwf mutant strains grown autotrophically or mixotrophically, twice the amount of xylulose-5-phosphate is synthesized during the Calvin cycle relative to ribose-5-phosphate in mixotrophical growth, with the epimerase being downregulated
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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nearest neighbor analyses of immunocytolocalization experiments indicate that glyceraldehyde-3-P dehydrogenase and phosphoribulokinase are located close to xylulose-5-P 3-epimerase in the pea leaf chloroplast stroma
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45900
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ultracentrifugation
50000
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sedimentation equilibrium experiments
55000
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cyt-RPEase, gel filtration
180000
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gel filtration
200000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 25966, calculation from nucleotide sequence
hexamer
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the thgree asymmetric subunits A, B and C for the hexamer by associating with subunits B‘, A‘, and C‘, respectively
octamer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 25% (w/v) PEG 3350, 100 mM Bis-Tris (pH 5.5), and 200 mM NaCl
crystals are produced with hanging drop method using 6 mg/ml cytosolic enzyme, 1.0 M ammonium sulfate, 50 mM Mops, pH 7.5, 1% w/v polyethylene glycol 400, 10 mM glycerol-3-phosphate and 5 mM L-arginine in the drop
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hanging drop vapor diffusion method
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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
crystals are grown using the microbatch technique from 22% methyl ether PEG 2000, 200 mM MgCl2, 100 mM MES pH 6.0. The crystals belong tp space group P2(1), with unit-cell parameters a = 82.6 A, b = 87.8 A, c = 97.8 A, beta = 114.6°, 1.6 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5
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24 h, 25°C, about 70% loss of activity
2230
7 - 8
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24 h, 25°C, stable
2230
9
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24 h, 25°C, about 20% loss of activity
2230
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
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2 min, stable
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
DL-alpha-glycerophosphate or ethanol stabilize the extremely labile recombinant enzyme, but are unable to reverse the spontaneous loss of activity
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drastically destabilized by 2-mercaptoethanol
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DTT destabilizes
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
ribulose-5-phosphate 3-epimerase is vulnerable to H2O2 damage in vivo. H2O2 rapidly oxidizes the Fe2+ in a Fenton reaction, the oxidized iron is released immediately, causing a loss of activity. When purified enzyme is loaded with Mn2+, Co2+, or Zn2+, there is no loss in activity when challenged with H2O2
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716784
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 0.5 M ammonium sulfate, stable for at least 2 months
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2°C, wether in crude extracts or highly purified, the recombinant enzyme is inherently unstable
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4°C, stable as ammonium precipitate for several weeks
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
lysate is applied to a chelating sepharose fast flow column charged with Ni2+, the N-terminal His tag is removed by thrombin cleavage
mutant enzymes D186A, D186N, D186E
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Ni-affinity column chromatography and Superdex G75 gel filtration
partial
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recombinant cytosolic enzyme
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recombinant His-tagged enzyme
B3WBA1
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, expression as His-tagged enzyme
B3WBA1
enzyme with half normal activity in a malformed and severely mentally retarded girl with a de novo interstitial deletion 46,XX.del(2)(q32.lq34). It is suggested that the gene for ribulose-phosphate 3-epimerase is located on the segment 2q32.1 to q34
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Escherichia coli clones harboring the cfxE gene show up to 19-fold-higher activities of ribulose-phosphate 3-epimerase
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expressed in Escherichia coli BL21(DE3) cells
expression in Escherichia coli
expression of cytosoli enzyme in Escherichia coli
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the enzyme for ribulose 5-phosphate epimerase is localized to chromosome X
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the gene encoding RPE is expressed in the Escherichia coli strain BL21 (DE3)
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the growth condition-dependent enzyme is present in the proteomes of wild-type and zwf strains and is downregulated under mixotrophic growth conditions
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D175A
inactive
D37A
the mutation almost abolishes the enzymatic activity
H35A
the mutation almost abolishes the enzymatic activity
H70A
completely insoluble
L12A
the mutation results in more than 50% decrease in the activity
M141A
the mutation results in about 30% decrease in the activity
M39A
the mutation results in about 10% decrease in the activity
M72A
the mutation results in an almost 50% decrease in the activity
S10A
the mutation almost abolishes the enzymatic activity
D186A
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KM-value for D-ribulose 5-phosphate is increased 10fold, turnover-number is decreased to less than 0.1% of the wild-type value
D186E
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KM-value for D-ribulose 5-phosphate is unaltered, turnover-number is decreased to less than 0.1% of the wild-type value
D186N
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KM-value for D-ribulose 5-phosphate is unaltered, turnover-number is decreased to less than 0.1% of the wild-type value
D176A
no detectable activity, substrate= 10 mM D-ribulose 5-phosphate
D36A
no detectable activity, substrate= 10 mM D-ribulose 5-phosphate
H34A
mutant discloses decreased affinity for Zn2+, kcat = 200/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2
H67A
mutant discloses decreased affinity for Zn2+, kcat = 270/sec, substrate = 10 mM D-ribulose 5-phosphate, +10 micromol/l ZnCl2
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
synthesis
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enzyme is involved in a cascade of eleven immobilized enzyme reactors in series used for the production of D-ribulose-1,5-bisphosphate from 3-phospho-D-glycerate
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