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
L-rhamnose degradation I
-
-
degradation of hexoses
-
-
Pentose and glucuronate interconversions
-
-
Fructose and mannose metabolism
-
-
Microbial metabolism in diverse environments
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-
SYSTEMATIC NAME
IUBMB Comments
L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
-
CAS REGISTRY NUMBER
COMMENTARY hide
9054-58-4
-
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
-
?
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
-
-
product ratio 44:56
-
?
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
-
-
-
D-Fructose-1,6-diphosphate
?
show the reaction diagram
-
1.8% of the activity with L-rhanmnulose 1-phosphate
-
-
-
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
-
-
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
-
-
HgCl2
-
reversible
L-Rhamnitol 1-phosphate
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-
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
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-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.1
dihydroxyacetone phosphate
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-
38.3
L-rhamnulose 1-phosphate
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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 25°C
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 25°C
0.005
-
mutant enzyme N32D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25°C
0.006
-
mutant enzyme S116D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25°C
0.2
-
mutant enzyme N29D, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25°C
3.3
-
enzyme activity in culture performed at 37°C
3.8
-
wild type enzyme, using L-rhamnulose-1-phosphate as substrate, at pH 7.0 and 25°C
4.2
-
enzyme activity in culture performed at 28°C
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
UNIPROT
ORGANISM
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
-
-
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
-
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
-
0-4°C, stable for at least 3 months
5049
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
sulfhydryl compounds stabilize
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-4°C, crystalline enzyme, containing 0.2-1.0% protein, stable for at least 3 months
-
0-4°C, pH 7.0, 0.01 M mercaptoethanol, stable for at least 3 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HR 16/40 afinity column chromatography
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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)
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expressed in Escherichia coli strain JM105
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expressed in Escherichia coli strain M-15
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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 (1544 entries)
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