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Ca2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Cu2+
-
the enzyme preparation contains a mixture of the following metals in order of decreasing abundance: Zn2+, Mn2+, Cu2+
Ni2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Zinc
-
the catalytic zinc residue is located at the interface between two adjacent subunits
additional information
-
His95 and His97 are likely metal ion ligands
Co2+
-
can replace Zn2+ in mutant enzyme Y229F and in wild-type enzyme, Km-value for wild-type enzyme is 0.00029 mM
Co2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Mg2+
-
poorly bound, weak activator, KM-value for wild-type enzyme is 1.35 mM
Mg2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Mn2+
-
can replace Zn2+ in mutant enzyme Y229F and in wild-type enzyme. Km-value for wild-type enzyme is 0.00054 mM
Mn2+
-
the enzyme preparation contains a mixture of the following metals in order of decreasing abundance: Zn2+, Mn2+, Cu2+
Mn2+
-
reactivated after EDTA treatment by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
Mn2+
-
in presence of the optimal concentration of Mn2+ the specific activity is 5times greater than that displayed by the crystalline enzyme as isolated and assayed in absence of added metal
Zn2+
-
H95N, H97N, and D76N mutant enzymes require exogenous metal ions for full activity
Zn2+
-
physiological activator, KM-value for wild-type enzyme is 0.00017 mM
Zn2+
-
the enzyme preparation contains a mixture of the following metals in order of decreasing abundance: Zn2+, Mn2+, Cu2+
Zn2+
-
divalent metal ion required. Reactivated by addition of divalent metal ion in decreasing order: Mn2+, Co2+, Ni2+, Ca2+, Zn2+, Mg2+
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0.047 - 1.2
L-ribulose 5-phosphate
0.047
L-ribulose 5-phosphate
-
37°C, pH 7.6, wild-type enzyme
0.0471
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM ZnCl2
0.06
L-ribulose 5-phosphate
-
wild type enzyme, Zn2+ form of enzyme plus 0.1 mM Zn2+
0.06
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, wild-type enzyme
0.086
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme E142Q
0.087
L-ribulose 5-phosphate
-
wild type enzyme, Zn2+ form of enzyme after dialysis
0.087
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, wild-type
0.091
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme H95N, activated by 0.1 mM ZnCl2
0.095
L-ribulose 5-phosphate
-
-
0.096
L-ribulose 5-phosphate
-
mutant H95N, Zn2+ form of enzyme plus 0.1 mM Zn2+
0.096
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, mutant enzyme H95N
0.1
L-ribulose 5-phosphate
-
-
0.1
L-ribulose 5-phosphate
-
L-ribulose 5-phosphate, mutant H97N, Zn2+ form of enzyme after dialysis
0.1
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme H95N
0.11
L-ribulose 5-phosphate
-
mutant D76N, Zn2+ form of enzyme after dialysis
0.11
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM CoCl2
0.11
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme D76N
0.129
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme Y229F, activated by 0.1 mM ZnCl2
0.132
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme H97N, activated by 0.1 mM ZnCl2
0.14
L-ribulose 5-phosphate
-
L-ribulose 5-phosphate, mutant H97N and D76N, Zn2+ form of enzyme plus 0.1 mM Zn2+
0.14
L-ribulose 5-phosphate
-
mutant H95N, Zn2+ form of enzyme after dialysis
0.14
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, mutant enzyme H97N or D76N
0.14
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme H97N
0.25
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme D76E
0.28
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme D120N
0.415
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM MnCl2
0.493
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM MgCl2
0.58
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme H218N
1.2
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme N28A
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0.0057 - 36.5
L-ribulose 5-phosphate
0.0057
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme D120N
0.0118
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme Y229F, activated by 0.1 mM ZnCl2
0.047
L-ribulose 5-phosphate
-
mutant H95N, Zn2+ form of enzyme after dialysis
0.047
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme H95N
0.048
L-ribulose 5-phosphate
-
mutant H97N, Zn2+ form of enzyme after dialysis
0.048
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme H97N
0.073
L-ribulose 5-phosphate
-
mutant D76N, Zn2+ form of enzyme after dialysis
0.073
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, mutant enzyme D76N
0.1
L-ribulose 5-phosphate
-
mutant H95N, Zn2+ form of enzyme plus 0.1 mM Zn2+
0.16
L-ribulose 5-phosphate
-
mutant D76N, Zn2+ form of enzyme plus 0.1 mM Zn2+
0.16
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, mutant enzyme D76N
0.183
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme H95N, activated by 0.1 mM ZnCl2
0.502
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM MgCl2
0.81
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme H218N
1
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme D76E
1.1
L-ribulose 5-phosphate
-
37°C, pH 7.6, wild-type enzyme
2.01
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme H97N, activated by 0.1 mM ZnCl2
2.14
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme E142Q
2.5
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme N28A
2.94
L-ribulose 5-phosphate
-
22°C, pH 7.5, mutant enzyme H97N, activated by 0.1 mM ZnCl2
2.94
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme E142Q
6.08
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM MgCl2
6.08
L-ribulose 5-phosphate
-
37°C, pH 7.6, mutant enzyme H218N
7.3
L-ribulose 5-phosphate
-
mutant H97N, Zn2+ form of enzyme plus 0.1 mM Zn2+
7.3
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, mutant enzyme H97N
17.3
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM ZnCl2
19.4
L-ribulose 5-phosphate
-
37°C, pH 7.6, wild-type enzyme
20.4
L-ribulose 5-phosphate
-
wild type enzyme, Zn2+ form of enzyme after dialysis
20.4
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis, wild-type
20.7
L-ribulose 5-phosphate
-
wild type enzyme, Zn2+ form of enzyme plus 0.1 mM Zn2+
21.8
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM CoCl2
22.4
L-ribulose 5-phosphate
-
37°C, pH 7.6, Zn2+-form after dialysis + 0.1 mM Zn2+, wild-type enzyme
36.5
L-ribulose 5-phosphate
-
22°C, pH 7.5, wild-type enzyme, activated by 0.1 mM MnCl2
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D120N
-
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
-
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
E142Q
-
the ratio of turnover number to Km-value is 17fold lower than that of the wild-type enzyme
H218N
-
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
-
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
-
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
-
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
D76N
-
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
D76N
-
the ratio of turnover number to Km-value is 348fold lower than that of the wild-type enzyme
H95N
-
the ratio of turnover number to Km-value is 24.1fold lower than that of the wild-type enzyme when activated with ZnCl2
H95N
-
the ratio of turnover number to Km-value is 676fold lower than that of the wild-type enzyme
H97N
-
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
H97N
-
13C isotope effects at pH 7 are 3.25% at C-3 and 2.69% at C4, compared to 1.85% and 1.5% for the wild-type enzyme
H97N
-
mutant enzyme with low levels of aldolase activity. The ratio of turnover number to Km-value is 479fold lower than that of the wild-type enzyme
H97N
-
the ratio of turnover number to Km-value is 4011fold lower than that of the wild-type enzyme when activated with ZnCl2
Y229F
-
13C isotope effects at pH 7 are 2.53% at C-3 and 1.99% at C4, compared to 1.85% and 1.5% for the wild-type enzyme
Y229F
-
the ratio of turnover number to Km-value is 182.5fold lower than that of the wild-type enzyme when activated with ZnCl2
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Davis, L.; Lee, N.; Glaser, L.
On the mechanism of the pentose phosphate epimerase
J. Biol. Chem.
247
5862-5866
1972
Escherichia coli
brenda
Burma, D.P.; Horecker, B.L.
Pentose fermentation by Lactobacillus plantarum. IV. L-Ribulose-5-phosphate 4-epimerase
J. Biol. Chem.
231
1053-1064
1958
Lactiplantibacillus plantarum
brenda
Wolin, M.J.; Simpson, F.J.; Wood, W.A.
Degradation of L-arabinose by Aerobacter aerogenes. III. Identification and properties of L-ribulose-5-phosphate 4-epimerase
J. Biol. Chem.
232
559-575
1958
Klebsiella aerogenes
brenda
Lee, N.; Patrick, J.W.; Masson, M.
Crystalline L-ribulose 5-phosphate 4-epimerase from Escherichia coli
J. Biol. Chem.
243
4700-4705
1968
Escherichia coli
brenda
Deupree, J.D.; Wood, W.A.
L-Ribulose 5-phosphate 4-epimerase of Aerobacter aerogenes. Evidence for nicotinamide adenine dinucleotide-independent 4-epimerization by the crystalline enzyme
J. Biol. Chem.
245
3988-3995
1970
Klebsiella aerogenes
brenda
Deupree, J.D.; Wood, W.A.
L-Ribulose 5-phosphate 4-epimerase from Aerobacter aerogenes. Evidence for a role of divalent metal ions in the epimerization reaction
J. Biol. Chem.
247
3093-3097
1972
Klebsiella aerogenes
brenda
Salo, W.L.; Fossitt, D.D.; Bevill, R.D.; Kirkwood, S.; Wood, W.A.
L-Ribulose 5-phosphate 4-epimerase from Aerobacter aerogenes. Kinetic isotope effect with tritiated substrate
J. Biol. Chem.
247
3098-3100
1972
Klebsiella aerogenes
brenda
LeBlanc, D.J.; Mortlock, R.P.
Regulation of the L-arabinose catabolic pathway in Aerobacter aerogenes
Arch. Biochem. Biophys.
156
390-396
1973
Klebsiella aerogenes
brenda
Deupree, J.; Wood, W.A.
L-Ribulose-5-phosphate 4-epimerase from Aerobacter aerogenes
Methods Enzymol.
41B
412-419
1975
Klebsiella aerogenes
-
brenda
Gielow, W.O.; Lee, N.
L-Ribulose-5-phosphate 4-epimerase from Escherichia coli
Methods Enzymol.
41B
419-423
1975
Escherichia coli
-
brenda
Lin, H.C.; Lei, S.P.; Studnicka, G.; Wilcox, G.
The araBAD operon of Salmonella typhimurium LT12. III. Nucleotide sequence of araD and its flanking regions, and primary stucture of its product, L-ribulose-5-phosphate 4-epimerase
Gene
34
129-134
1985
Salmonella enterica subsp. enterica serovar Typhimurium
brenda
Mineno, J.; Fukui, H.; Ishino, Y.; Kato, I.; Shinagawa, H.
Nucleotide sequence of the araD gene of Escherichia coli K12 encoding the L-ribulose 5-phosphate 4-epimerase
Nucleic Acids Res.
18
6722
1990
Escherichia coli
brenda
Andersson, A.; Schneider, G.; Lindqvist, Y.
Purification and preliminary X-ray crystallographic studies of recombinant L-ribulose-5-phosphate 4-epimerase from Escherichia coli
Protein Sci.
4
1648-1650
1995
Escherichia coli
brenda
Johnson, A.E.; Tanner, M.E.
Epimerization via carbon - carbon bond cleavage. L-Ribulose-5-phosphate 4-epimerase as a masked class II aldolase
Biochemistry
37
5746-5754
1998
Escherichia coli
brenda
Sa-Nogueira, I.; Nogueira, T.V.; Soares, S.; de Lencastre, H.
The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression
Microbiology
143
957-969
1997
Bacillus subtilis
brenda
Lee, L.V.; Vu, M.V.; Cleland, W.W.
13C and deuterium isotope effects suggest an aldol cleavage mechanism for L-ribulose-5-phosphate 4-epimerase
Biochemistry
39
4808-4820
2000
Escherichia coli
brenda
Lee, L.V.; Poyner, R.R.; Vu, M.V.; Cleland, W.W.
Role of metal ions in the reaction catalyzed by L-ribulose-5-phosphate 4-epimerase
Biochemistry
39
4821-4830
2000
Escherichia coli
brenda
Luo, Y.; Samuel, J.; Mosimann, S.C.; Lee, J.E.; Tanner, M.E.; Strynadka, N.C.
The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization
Biochemistry
40
14763-14771
2001
Escherichia coli
brenda
Samuel, J.; Luo, Y.; Morgan, P.M.; Strynadka, N.C.; Tanner, M.E.
Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase
Biochemistry
40
14772-14780
2001
Escherichia coli
brenda
Kawaguchi, H.; Sasaki, M.; Vertes, A.A.; Inui, M.; Yukawa, H.
Engineering of an L-arabinose metabolic pathway in Corynebacterium glutamicum
Appl. Microbiol. Biotechnol.
77
1053-1062
2008
Corynebacterium glutamicum
brenda
Wiedemann, B.; Boles, E.
Codon-optimized bacterial genes improve L-arabinose fermentation in recombinant Saccharomyces cerevisiae
Appl. Environ. Microbiol.
74
2043-2050
2008
Escherichia coli
brenda
Kawaguchi, H.; Sasaki, M.; Vertes, A.A.; Inui, M.; Yukawa, H.
Identification and functional analysis of the gene cluster for L-arabinose utilization in Corynebacterium glutamicum
Appl. Environ. Microbiol.
75
3419-3429
2009
Corynebacterium glutamicum (C4B4W3)
brenda