Information on EC 5.1.3.4 - L-ribulose-5-phosphate 4-epimerase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.1.3.4
-
RECOMMENDED NAME
GeneOntology No.
L-ribulose-5-phosphate 4-epimerase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-Ribulose 5-phosphate = D-xylulose 5-phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
epimerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Ascorbate and aldarate metabolism
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L-arabinose degradation I
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L-ascorbate degradation I (bacterial, anaerobic)
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L-ascorbate degradation II (bacterial, aerobic)
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L-lyxose degradation
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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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degradation of pentoses
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SYSTEMATIC NAME
IUBMB Comments
L-ribulose-5-phosphate 4-epimerase
Requires a divalent cation for activity.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-19-5
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
enzyme is part of the araBDA gene L-arabinose catabolism cluster
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
L-Ribulose 5-phosphate
?
show the reaction diagram
L-Ribulose 5-phosphate
D-Xylulose 5-phosphate
show the reaction diagram
additional information
?
-
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
L-Ribulose 5-phosphate
?
show the reaction diagram
L-Ribulose 5-phosphate
D-Xylulose 5-phosphate
show the reaction diagram
C4B4W3
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Cu2+
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the enzyme preparation contains a mixture of the following metals in order of decreasing abundance: Zn2+, Mn2+, Cu2+
Ni2+
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divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Zinc
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the catalytic zinc residue is located at the interface between two adjacent subunits
additional information
-
His95 and His97 are likely metal ion ligands
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,3-dimercapto-1-propanol
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8-Hydroxyquinoline sulfonate
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EDTA
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reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
glycoaldehyde phosphate
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competitive inhibitor of mutant enzyme H97N but not of the wild-type enzyme
glycolaldehyde
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glycolaldehyde phosphate
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competitive inhibition of H97N mutant enzyme, no inhibition of wild type enzyme
mercaptoethanol
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-
additional information
-
inactivated by Neurospora diphosphopyridine nucleotidase
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.047 - 1.2
L-ribulose 5-phosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0057 - 36.5
L-ribulose 5-phosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.37
glycolaldehyde
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37C, pH 7.6, mutant enzyme H97N, with L-ribulose 5-phosphate as substrate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
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at pH 7 and above
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 10
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6: about 65% of maximal activity, 7 and above: maximal activity
6 - 9
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6: about 50% of maximal activity, 7-9: maximal activity
7 - 10
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7: about 30% of maximal activity, 10: about 85% of maximal activity
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25522
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4 * 25522, electrospray mass spectrometry
35000
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3 * 35000, sedimentation equilibrium measurement after dissociation of the enzyme with urea or performic acid oxidation
103000
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sedimentation equilibrium measurement
105000
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sedimentation equilibrium measurement
114000
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high speed equilibrium analysis
127000
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wild-type enzyme and mutant enzymes H97N, D76N and H95N, gel filtration
additional information
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determination of nucleotide sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
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4 * 25522, electrospray mass spectrometry
trimer
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3 * 35000, sedimentation equilibrium measurement after dissociation of the enzyme with urea or performic acid oxidation
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method of recombinant enzyme, the enzyme crystallizes as a homotetramer with C4 symmetry. Each subunit has a single domain comprised of a central beta-sheet flanked on either side by layers of alpha-helices
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 55
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thermal denaturation themperature of wild-type enzyme and mutant enzymes H97N, D76N and H95N
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, stable
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
wild-type and mutant enzymes expressed in Escherichia coli Y1090
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme is expressed in Escherichia coli
expression in Escherichia coli
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overexpression
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
araD deletion mutants are unable to grow on L-arabinose, although these mutants grew on D-glucose with the same specific growth rate as the wild-type strain
levels of expression of araD is more than 43fold higher when the wild-type strain is grown on L-arabinose than when it is grown on D-glucose, significantly higher levels of expression of the gene is also observed for wild-type cells grown on L-arabinose plus D-glucose
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D120N
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3000fold decrease in the value of turnover number. The structure is indistinguishable from that of the wild-type enzyme and the decrease in activity is not simply due to a strutural perturbation of active site. The ratio of turnover number to Km-value is 20750fold lower than that of the wild-type enzyme
D76E
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the ratio of turnover number to Km-value is 104fold lower than that of the wild-type enzyme,2.2fold decrease in backgroud aldolase activity compared to wild-type enzyme
D76N
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site-directed mutants in which the putative metal ion ligand is modified: H95N, H97N, D76N. The mutant enzymes require exogenous metal ions for full activity. Their turnover numbers are greatly reduced whereas the Km-values are only moderately affected. Low levels of aldolase activity are observed with the H97N mutant, but not with D76N or the H95N mutants. The H97N mutant enzyme catalyzes the condensation of dihydroxyacetone and glycolaldehyde phosphate to produce a mixture of L-ribulose 5-phosphate and D-xylulose 5-phosphate; the ratio of turnover number to Km-value is 348fold lower than that of the wild-type enzyme
E142Q
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the ratio of turnover number to Km-value is 17fold lower than that of the wild-type enzyme
H218N
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15fold decrease in background aldolase activity compared to wild-type enzyme. The ratio of turnover number to Km-value is 296fold lower than that of the wild-type enzyme
H59N
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site-directed mutants in which the putative metal ion ligand is modified: H95N, H97N, D76N. The mutant enzymes require exogenous metal ions for full activity. Their turnover numbers are greatly reduced whereas the Km-values are only moderately affected. Low levels of aldolase activity are observed with the H97N mutant, but not with D76N or the H95N mutants. The H97N mutant enzyme catalyzes the condensation of dihydroxyacetone and glycolaldehyde phosphate to produce a mixture of L-ribulose 5-phosphate and D-xylulose 5-phosphate
K42M
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the ratio of turnover number to Km-value is 12969fold lower than that of the wild-type enzyme, 5.3fold increase in backgroud aldolase activity compared to wild-type enzyme
N28A
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the ratio of turnover number to Km-value is 198fold lower than that of the wild-type enzyme, 10.2fold increase in backgroud aldolase activity compared to wild-type enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
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improvement of a bacterial L-arabinose utilization pathway consisting of L-arabinose isomerase from Bacillus licheniformis and L-ribulokinase and L-ribulose-5-phosphate 4-epimerase from Escherichia coli after expression of the corresponding genes in Saccharomyces cerevisiae. After adaptation of codon usage, yeast transformants show strongly improved L-arabinose conversion rates. The ethanol production rate from L-arabinose can be increased more than 2.5fold from 0.014 g ethanol per h and g dry weight to 0.036 g ethanol per h and g dry weight and the ethanol yield can be increased from 0.24 g ethanol per g consumed L-arabinose to 0.39 g ethanol per g consumed L-arabinose
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