Information on EC 4.1.2.19 - rhamnulose-1-phosphate aldolase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.2.19
-
RECOMMENDED NAME
GeneOntology No.
rhamnulose-1-phosphate aldolase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-Rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
addition
-
syn-aldol addition
aldol addition
-
-
condensation
-
-
-
-
elimination
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Fructose and mannose metabolism
-
-
L-rhamnose degradation I
-
-
Microbial metabolism in diverse environments
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Pentose and glucuronate interconversions
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degradation of hexoses
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SYSTEMATIC NAME
IUBMB Comments
L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
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CAS REGISTRY NUMBER
COMMENTARY hide
9054-58-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Arthrobacter pyridinolis
-
-
-
Manually annotated by BRENDA team
strain K12
-
-
Manually annotated by BRENDA team
strain K40
-
-
Manually annotated by BRENDA team
strain W3110
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,3S)-3-methyl-1-oxopentane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-((S)-sec-butyl)-3,4-diol + N-ethyl-(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-((S)-sec-butyl)-3,4-diol
show the reaction diagram
-
-
product ratio 55:45
-
?
(benzyloxy)acetaldehyde + dihydroxyacetone
(3R,4S)-5-(benzyloxy)-1,3,4-trihydroxypentan-2-one + (3R,4R)-5-(benzyloxy)-1,3,4-trihydroxypentan-2-one
show the reaction diagram
-
favored direction of reaction
-
-
r
(R)-1-oxobutane-2-benzylcarbamate
(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-ethyl-3,4-diol + (2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-ethyl-3,4-diol + N-ethyl-(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-ethyl-3,4-diol + N-ethyl-(2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-ethyl-3,4-diol
show the reaction diagram
-
-
product ratio 48:30:11:11
-
?
(R)-1-oxohexane-2-benzylcarbamate
(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + (2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + N-ethyl-(2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + N-ethyl-(2S,3S,4S,5R)-2-(hydroxymethyl)-pyrrolidine-5-propyl-3,4-diol
show the reaction diagram
-
-
product ratio 28:63:5:5
-
?
(R)-1-oxopentane-2-benzylcarbamate
(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + (2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + N-ethyl-(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol + N-ethyl-(2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol
show the reaction diagram
-
-
product ratio 44:34:11:10
-
?
(R)-3-methyl-1-oxobutane-2-benzylcarbamate
(2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-isopropyl-3,4-diol
show the reaction diagram
-
-
-
-
?
(R)-4-methyl-1-oxopentane-2-benzylcarbamate
(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol + (2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol + N-ethyl-(2R,3S,4R,5R)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol + N-ethyl-(2S,3S,4S,5R)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol
show the reaction diagram
-
-
product ratio 32:43:16.9
-
?
(S)-1-oxo-3-phenylpropan-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-benzyl-3,4-diol
show the reaction diagram
-
-
-
-
?
(S)-1-oxobutane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-ethyl-3,4-diol
show the reaction diagram
-
-
-
-
?
(S)-1-oxohexane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-butyl-3,4-diol + (2S,3S,4R,5S)-2-(hydroxymethyl)pyrrolidine-5-butyl-3,4-diol
show the reaction diagram
-
-
product ratio 93:7
-
?
(S)-1-oxopentane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-propyl-3,4-diol
show the reaction diagram
-
-
-
-
?
(S)-3-methyl-1-oxobutane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-isopropyl-3,4-diol + N-ethyl-(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-isopropyl-3,4-diol
show the reaction diagram
-
-
product ratio 84:16
-
?
(S)-4-methyl-1-oxopentane-2-benzylcarbamate
(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol + (2S,3S,4R,5S)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol + N-ethyl-(2S,3S,4S,5S)-2-(hydroxymethyl)pyrrolidine-5-isobutyl-3,4-diol
show the reaction diagram
-
-
product ratio 71:6:23
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?
2-methyl-1-oxopropane-2-benzylcarbamate
(2S,3S,4S)-2-(hydroxymethyl)pyrrolidine-5-dimethyl-3,4-diol + (2R,3S,4R)-2-(hydroxymethyl)pyrrolidine-5-dimethyl-3,4-diol
show the reaction diagram
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-
product ratio 44:56
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?
6-Deoxy-L-sorbose 1-phosphate
Glycerone phosphate + D-lactaldehyde
show the reaction diagram
-
0.8% of the activity with L-rhamnulose 1-phosphate
-
-
-
benzyl (2-oxoethyl)carbamate + dihydroxyacetone
benzyl [(2S,3R)-2,3,5-trihydroxy-4-oxopentyl]carbamate + benzyl [(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]carbamate
show the reaction diagram
-
favored direction of reaction
-
-
r
benzyl [(2R)-1-oxopropan-2-yl]carbamate + dihydroxyacetone
benzyl [(2R,3S,4R)-3,4,6-trihydroxy-5-oxohexan-2-yl]carbamate + benzyl [(2R,3R,4R)-3,4,6-trihydroxy-5-oxohexan-2-yl]carbamate
show the reaction diagram
-
favored direction of reaction
-
-
r
D-Fructose 1-phosphate
?
show the reaction diagram
-
1.7% of the activity with L-rhanmnulose 1-phosphate
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-
-
D-Fructose-1,6-diphosphate
?
show the reaction diagram
-
1.8% of the activity with L-rhanmnulose 1-phosphate
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-
-
D-Ribulose 1,5-diphosphate
?
show the reaction diagram
-
1.3% of the activity with L-rhanmnulose 1-phosphate
-
-
-
dihydroxyacetone + L-lactaldehyde
L-rhamnulose 1-phosphate
show the reaction diagram
-
favored direction of reaction
-
-
r
dihydroxyacetone phosphate + L-lactaldehyde
?
show the reaction diagram
-
-
-
-
?
dihydroxyacetone phosphate + L-lactaldehyde
L-rhamnulose 1-phosphate
show the reaction diagram
-
favored direction of reaction
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-
r
dihydroxyacetone phosphate + L-lactaldehyde
L-rhamnulose-1-phosphate
show the reaction diagram
-
-
-
-
r
dihydroxyacetone phosphate + N-Cbz-(2R)-2-amino-3-methylbutanal
N-Cbz-5-amino-1,3,4-trihydroxyoctan-2-one
show the reaction diagram
-
-
yield 93%, ratio of (3R,4S) to (3S,4R) product is 2:98
-
?
dihydroxyacetone phosphate + N-Cbz-(2S)-2-amino-3-methylbutanal
N-Cbz-5-amino-1,3,4-trihydroxyoctan-2-one
show the reaction diagram
-
-
yield 93%, ratio of (3R,4S) to (3S,4R) product is 98:2
-
?
dihydroxyacetone phosphate + N-Cbz-(2S)-2-aminobutanal
N-Cbz-5-amino-1,3,4-trihydroxyheptan-2-one
show the reaction diagram
-
-
yield 94%, ratio of (3R,4S) to (3S,4R) product is 98:2
-
?
dihydroxyacetone phosphate + N-Cbz-(2S)-2-aminopropanal
N-Cbz-5-amino-1,3,4-trihydroxyhexan-2-one
show the reaction diagram
-
-
yield 99%, ratio of (3R,4S) to (3S,4R) product is 98:2
-
?
dihydroxyacetone phosphate + N-Cbz-aminoacetaldehyde
N-Cbz-5-amino-1,3,4-trihydroxypentan-2-one
show the reaction diagram
-
yield 91%, ratio of (3R,4S) to (3S,4R) product is 94:6
yield 91%, ratio of (3R,4S) to (3S,4R) product is 94:6
-
?
Glycerone phosphate + (S)-lactaldehyde
L-Rhamnulose 1-phosphate
show the reaction diagram
Glycerone phosphate + acetaldehyde
5-Deoxy-L-xylulose 1-phosphate
show the reaction diagram
Glycerone phosphate + D-glyceraldehyde
D-Sorbose 1-phosphate
show the reaction diagram
Glycerone phosphate + D-lactaldehyde
6-Deoxy-D-sorbose 1-phosphate
show the reaction diagram
Glycerone phosphate + formaldehyde
D-Erythrulose 1-phosphate
show the reaction diagram
Glycerone phosphate + glycolaldehyde
L-Xylulose 1-phosphate
show the reaction diagram
L-Rhamnulose 1-phosphate
?
show the reaction diagram
L-rhamnulose 1-phosphate
dihydroxyacetone phosphate + L-lactaldehyde
show the reaction diagram
-
-
-
-
r
L-Rhamnulose 1-phosphate
Glycerone phosphate + (S)-lactaldehyde
show the reaction diagram
L-Sorbose 1-phosphate
Glycerone phosphate + D-glyceraldehyde
show the reaction diagram
N-formylglycinal + dihydroxyacetone
N-[(2S,3R)-2,3,5-trihydroxy-4-oxopentyl]formamide + N-[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]formamide
show the reaction diagram
-
-
-
-
r
Xylulose 1-phosphate
Glycerone phosphate + glycoaldehyde
show the reaction diagram
additional information
?
-
-
RhuA is highly stereoselective with (S)-N-Cbz-2-aminoaldehydes (90-100% syn (i.e., 3R,4S) adduct), whereas those with R configuration give mixtures of anti/syn adducts, for iPr and iBu substituents, RhuA furnishes the anti adduct with high stereoselectivity
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-
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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
L-Rhamnulose 1-phosphate
?
show the reaction diagram
L-rhamnulose 1-phosphate
dihydroxyacetone phosphate + L-lactaldehyde
show the reaction diagram
-
-
-
-
r
L-Rhamnulose 1-phosphate
Glycerone phosphate + (S)-lactaldehyde
show the reaction diagram
-
-
-
-
r
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
restores activity of the enzyme after inactivation by dialysis against chelating agents or by treatment with SDS and 2-mercaptoethanol
Cs+
-
Na+, Cs+, NH4+, Rb+ and K+, in the order of increasing effectiveness markedly enhance activity
K+
-
Na+, Cs+, NH4+, Rb+ and K+, in the order of increasing effectiveness markedly enhance activity
Na+
-
Na+, Cs+, NH4+, Rb+ and K+, in the order of increasing effectiveness markedly enhance activity
NH4+
-
Na+, Cs+, NH4+, Rb+ and K+, in the order of increasing effectiveness markedly enhance activity
Ni2+
-
restores activity of the enzyme after inactivation by dialysis against chelating agents or by treatment with SDS and 2-mercaptoethanol
Rb+
-
Na+, Cs+, NH4+, Rb+ and K+, in the order of increasing effectiveness markedly enhance activity
Zn
-
contains 2 gatom of zinc per mol of enzyme; zinc metalloenzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
2,2'-dipyridyl
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-
5,5'-dithiobis(2-nitrobenzoate)
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-
8-hydroxyquinoline 5-sulfonic acid
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-
HgCl2
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reversible
L-Rhamnitol 1-phosphate
-
-
p-mercuribenzoate
phosphate
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the aldol addition of dihydroxyacetobe is strongly inhibited by phosphate
SDS
-
competitive with L-rhamnulose 1-phosphate or glycerone phosphate, noncompetitive with L-lactaldehyde
sulfate
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-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
the enzyme contains 12 sulfhydryl groups per molecule
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.8
D-Sorbose 1-phosphate
-
-
1125 - 1339
dihydroxyacetone
0.6 - 7
dihydroxyacetone phosphate
0.2 - 3
glycerone phosphate
0.1 - 6
L-lactaldehyde
0.2 - 10
L-rhamnulose 1-phosphate
0.2
L-xylulose 1-phosphate
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.1
dihydroxyacetone phosphate
Escherichia coli
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-
38.3
L-rhamnulose 1-phosphate
Escherichia coli
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-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1
Co2+
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.5
phosphate
Escherichia coli
-
wild type enzyme, at pH 7.0 and 25C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.002
-
mutant enzyme S75D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25C
0.005
-
mutant enzyme N32D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25C
0.006
-
mutant enzyme S116D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25C
0.2
-
mutant enzyme N29D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25C
3.3
-
enzyme activity in culture performed at 37C
3.8
-
wild type enzyme, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25C
4.2
-
enzyme activity in culture performed at 28C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
pH 6.0: about 30% of maximal activity, pH 9.9: about 50% of maximal activity
6.3 - 9
-
about 50% of maximal activity at pH 6.3 and at pH 9.0
8.5 - 9.9
-
pH 8.5: about 50% of maximal activity, pH 9.9: about 70% of maximal activity
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32000
-
determined by SDS-PAGE
35000
-
4 * 35000
130000 - 140000
-
sucrose density gradient centrifugation
135000
-
gel filtration
140000
-
gel filtration, density gradient centrifugation
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
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-
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop method, crystallizes in space group P3(2)21
-
mutant enzymes by hanging drop vapour diffusion method, with 100 mM sodium acetate pH 4.5, 50% (v/v) ethylene glycol and 5% (w/v) PEG1000
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structure established at 1.35 A resolution in a crystal form that is obtained by a surface mutation and has one subunit of the C4-symmetric tetramer in the asymmetric unit. Crystals of the wild-type enzyme with their 20 crystallographically asymmetric subunits diffract to only 2.7 A resolution are much too complex for a convenient analysis of structural modifications. For both reasons, a more suitable crystal form is obtained by producing the six point mutants W8T, Q51R, Q52E, D98Y, E192A and E254R at the protein surface far away from the active center
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
0-4C, stable for at least 3 months
5049
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
sulfhydryl compounds stabilize
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-4C, crystalline enzyme, containing 0.2-1.0% protein, stable for at least 3 months
-
0-4C, pH 7.0, 0.01 M mercaptoethanol, stable for at least 3 months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HR 16/40 afinity column chromatography
-
only 55% of immobilization yield is achieved when immobilized metal affinity chromatography is used to purify and immobilize RhuA from cellular lysate in a single step
-
Superdex 200 gel filtration
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli strain BL21 (DE3)
-
expressed in Escherichia coli strain JM105
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expressed in Escherichia coli strain M-15
-
expression in Escherichia coli cells
-
His-tagged enzyme is expressed in Escherichia coli M15DELTAglyA cells
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overexpression in Escherichia coli
-
overexpression in Escherichia coli cells
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E117Q
-
0.1% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 0.04% of the wild-type ratio
E171A
-
0.4% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 0.3% of the wild-type ratio
E171Q
-
0.4% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 0.1% of the wild-type ratio
E171S
-
2% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 0.7% of the wild-type ratio
E192A
-
as active as the wild-type enzyme with L-rhamnulose 1-phosphate
G264Stop
-
75% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as 23% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 7% of the wild-type ratio
K15W
-
reduced activity
K15Y
-
reduced activity
K248G/R253A/E254A/E192A
-
reduced activity
L84W
-
reduced activity
N29A
-
4% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 0.9% of the wild-type ratio
N29D
-
the mutant shows 5.3% of the wild type activity, the mutation increases by 3fold the Vappmax of aldol addition reactions of dihydroxyacetone to other aldehyde acceptors rather than the natural L-lactaldehyde
N32D
-
the mutant shows 0.1% of the wild type activity
Q11W
-
reduced activity
R28S
-
9% of the activity of the wild-type enzyme with L-rhamnulose 1-phosphate as substrate, the ratio of turnover number to Km-value is 2% of the wild-type ratio
S116D
-
the mutant shows 0.2% of the wild type activity
S75D
-
the mutant shows 0.1% of the wild type activity
T115D
-
completely inactive
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
Show AA Sequence (1334 entries)
Please use the Sequence Search for a specific query.