Information on EC 4.1.3.39 - 4-hydroxy-2-oxovalerate aldolase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.3.39
-
RECOMMENDED NAME
GeneOntology No.
4-hydroxy-2-oxovalerate aldolase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
2-oxopentenoate degradation
-
-
Benzoate degradation
-
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Dioxin degradation
-
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Metabolic pathways
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Microbial metabolism in diverse environments
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Phenylalanine metabolism
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Xylene degradation
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3-phenylpropionate degradation
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SYSTEMATIC NAME
IUBMB Comments
4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Requires Mn2+ for maximal activity [1]. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH [1]. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase [4,5].
CAS REGISTRY NUMBER
COMMENTARY hide
37325-52-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
nahKLMO operon; wild-type strain NCIMB9816, gene nahM
SwissProt
Manually annotated by BRENDA team
strain KB35B
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
-
polychlorinated biphenyl degradation pathway
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(4R)-4-hydroxy-2-oxopentanoate
acetaldehyde + pyruvate
show the reaction diagram
-
-
-
-
r
(4S)-4-hydroxy-2-oxopentanoate
acetaldehyde + pyruvate
show the reaction diagram
-
-
-
-
r
(S)-4-hydroxy-2-oxohexanoate
propanal + pyruvate
show the reaction diagram
(S)-4-hydroxy-2-oxopentanoate
ethanal + pyruvate
show the reaction diagram
(S)-4-hydroxy-2-oxopentanoate
propanal + pyruvate
show the reaction diagram
-
-
-
-
?
4-hydroxy-2-oxo-4-benzylbutanoate
benzaldehyde + pyruvate
show the reaction diagram
-
-
-
?
4-hydroxy-2-oxo-isoheptanoate
isobutyraldehyde + pyruvate
show the reaction diagram
-
-
-
?
4-hydroxy-2-oxoheptanoate
butyraldehyde + pyruvate
show the reaction diagram
-
-
-
?
4-hydroxy-2-oxohexanoate
propionaldehyde + pyruvate
show the reaction diagram
4-hydroxy-2-oxovalerate
acetaldehyde + pyruvate
show the reaction diagram
4-hydroxy-2-oxovalerate
pyruvate + acetaldehyde
show the reaction diagram
butyraldehyde + pyruvate
4-hydroxy-2-oxoheptanoate
show the reaction diagram
-
-
-
-
r
hexaldehyde + pyruvate
4-hydroxy-2-oxononanoate
show the reaction diagram
-
-
-
-
r
pentaldehyde + pyruvate
4-hydroxy-2-oxooctanoate
show the reaction diagram
-
-
-
-
r
propionaldehyde + pyruvate
4-hydroxy-2-oxohexanoate
show the reaction diagram
-
-
-
-
r
pyruvate + (R,S)-glyceraldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + acetaldehyde
(4S)-4-hydroxy-2-oxovalerate
show the reaction diagram
-
-
-
-
?
pyruvate + acetaldehyde
(4S)-hydroxy-2-oxopentanoate
show the reaction diagram
-
-
-
?
pyruvate + acetaldehyde
4-hydroxy-2-oxopentanoate
show the reaction diagram
-
-
-
?
pyruvate + butyraldehyde
?
show the reaction diagram
pyruvate + glycolaldehyde
4,5-dihydroxy-2-oxo-pentanoic acid
show the reaction diagram
pyruvate + glycolaldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + isobutyraldehyde
?
show the reaction diagram
pyruvate + pentaldehyde
?
show the reaction diagram
-
-
-
?
pyruvate + propionaldehyde
?
show the reaction diagram
pyruvate + succinic semialdehyde
(4RS)-4-hydroxy-2-oxoheptane-1,7-dioate
show the reaction diagram
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racemic product
-
?
pyruvate + succinic semialdehyde
?
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
(S)-4-hydroxy-2-oxohexanoate
propanal + pyruvate
show the reaction diagram
(S)-4-hydroxy-2-oxopentanoate
ethanal + pyruvate
show the reaction diagram
4-hydroxy-2-oxovalerate
acetaldehyde + pyruvate
show the reaction diagram
4-hydroxy-2-oxovalerate
pyruvate + acetaldehyde
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADH
-
BphI is activated in the presence of the BphJ cofactor, NADH, by about 5fold
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
15.4% activity with 1 mM Ni2+ compared to Mn2+; 35.1% activity with 1 mM Mg2+ compared to Mn2+; 59.5% activity with 1 mM Co2+ compared to Mn2+; 76% activity with 1 mM Ni2+ compared to Mn2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-ketobutanoate
2-ketopentanoate
4-methyl-2-oxopentanoate
glyoxylate
pyruvate
Zn2+
-
strong inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
BphJ
-
the aldehyde dehydrogenase BphJ coordinates the catalytic activity of BphI through allostery rather than through aldehyde channeling
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HsaG
the enzyme is active only in complex with the dehydrogenase HsaG
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NAD+
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stimulates slightly
NADH
-
stimulates
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.012 - 0.013
(4R)-4-hydroxy-2-oxopentanoate
0.013 - 0.228
(4S)-4-hydroxy-2-oxopentanoate
88.6
(R,S)-glyceraldehyde
pH 8.0, 25°C
0.0048
(S)-4-hydroxy-2-oxohexanoate
in 100 mM HEPES (pH 8.0), 0.4 mM NADH, 1 mM MgCl2, at 25°C
0.0044 - 0.158
(S)-4-hydroxy-2-oxopentanoate
62.9 - 80.5
acetaldehyde
13.4 - 323
Butyraldehyde
33.3 - 124.6
glycolaldehyde
24.8 - 33.3
pentaldehyde
16.8 - 136
propionaldehyde
11 - 20.2
pyruvate
73.8
Succinic semialdehyde
pH 8.0, 25°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.131 - 0.17
(4R)-4-hydroxy-2-oxopentanoate
0.089 - 4.07
(4S)-4-hydroxy-2-oxopentanoate
5.6
(R,S)-glyceraldehyde
Escherichia coli
Q47098
pH 8.0, 25°C
0.38
(S)-4-hydroxy-2-oxohexanoate
Mycobacterium tuberculosis
P9WMK5
in 100 mM HEPES (pH 8.0), 1 mM MgCl2, at 25°C
0.41 - 4.07
(S)-4-hydroxy-2-oxopentanoate
0.86 - 205.4
acetaldehyde
0.26 - 132.5
Butyraldehyde
0.4 - 175.5
glycolaldehyde
0.13 - 0.58
pentaldehyde
0.29 - 358.4
propionaldehyde
0.32 - 1.2
pyruvate
64.9
Succinic semialdehyde
Escherichia coli
Q47098
pH 8.0, 25°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10.4 - 14.1
(4R)-4-hydroxy-2-oxopentanoate
4449
0.012 - 44.7
(4S)-4-hydroxy-2-oxopentanoate
2805
0.063
(R,S)-glyceraldehyde
Escherichia coli
Q47098
pH 8.0, 25°C
40689
79.1
(S)-4-hydroxy-2-oxohexanoate
Mycobacterium tuberculosis
P9WMK5
in 100 mM HEPES (pH 8.0), 0.4 mM NADH, 1 mM MgCl2, at 25°C
28964
93.1
(S)-4-hydroxy-2-oxopentanoate
Mycobacterium tuberculosis
P9WMK5
in 100 mM HEPES (pH 8.0), 0.4 mM NADH, 1 mM MgCl2, at 25°C
5073
0.00042 - 13.4
acetaldehyde
90
0.00079 - 9.9
Butyraldehyde
499
0.0037 - 5.27
glycolaldehyde
604
0.00001 - 0.00013
hexaldehyde
6132
0.0005
Isobutyraldehyde
Paraburkholderia xenovorans LB400
P51015
at 25°C with 120 microg of BphI, 2 mM MnCl2 and 100 mM pyruvate
1646
0.00033 - 0.0233
pentaldehyde
3401
0.00673 - 13.2
propionaldehyde
273
0.0159 - 0.0915
pyruvate
31
0.5 - 22.5
Succinic semialdehyde
809
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.34 - 0.5
2-ketobutanoate
1.09 - 3.6
2-ketopentanoate
2.71 - 6.98
4-methyl-2-oxopentanoate
0.21 - 0.4
glyoxylate
0.51 - 0.55
pyruvate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.015 - 2.3
recombinant enzyme in extracts of different recombinant strains, activity depends on the plasmid vector used for expression and the aldehyde dehydrogenase, EC 1.2.1.10, overview
4.2
-
purified enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.5 - 9
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 9
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-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9)
Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32500
-
1 * 32500 + 1 * 37500, active unit is an enzyme complex of aldehyde dehydrogenase and 4-hydroxy-2-ketovalerate aldolase, SDS-PAGE and crystal structure
35000
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2 * 35000 + 2 * 40000, enzyme complex of aldehyde dehydrogenase and 4-hydroxy-2-ketovalerate aldolase, SDS-PAGE
37500
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1 * 32500 + 1 * 37500, active unit is an enzyme complex of aldehyde dehydrogenase and 4-hydroxy-2-ketovalerate aldolase, SDS-PAGE and crystal structure
38000
2 * 38000, SDS-PAGE
40000
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2 * 35000 + 2 * 40000, enzyme complex of aldehyde dehydrogenase and 4-hydroxy-2-ketovalerate aldolase, SDS-PAGE
148000
-
enzyme in complex with aldehyde dehydrogenase, EC 1.2.1.10, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complex with HsaG, sitting drop vapor diffusion method, using 18% (w/v) PEG 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 10% glycerol, and 10 mM sodium oxalate
purified enzyme complex of 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating), protein solution contains 9 mg/ml protein in 50 mM Tris-HCl, pH 7.4, 1 mM DTT, and 2 mM NAD+, mixing of equal volumes of 0.001 ml of protein and reservoir solutions, the latter contains 15% PEG 8000, 100 mM ammonium sulfate, and 100 mM PIPES, pH 7.5, 3 days, soaking of crystals in 5 mM samarium acetate and 0.25 mM PCMBS, X-ray diffraction structure determination and analysis at 2.1 A resolution
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purified selenomethionine-labeled enzyme complex of 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating), protein solution contains 9 mg/ml protein in 50 mM Tris-HCl, pH 7.4, 1 mM DTT, and 2 mM NAD+, mixing of equal volumes of 0.001 ml of protein and reservoir solutions, the latter contains 18% PEG 8000, 100 mM ammonium sulfate, and 100 mM PIPES, pH 7.5, 3 days, crystals are used for microseeding, cryoprotection by soaking in mother liquor with 20% v/v 2-methyl-2,4-pentanediol, X-ray diffraction structure determination and analysis at 1.7 A resolution
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, purified native enzyme, stable for at least 6 months
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4-6°C, purified native enzyme, stable for at least 6 days
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
co-purification with aldehyde dehydrogenase, EC 1.2.1.10, to homogeneity in a 3-step chromatographic procedure involving NAD+ affinity chromatography
-
co-purification with aldehyde dehydrogenase, EC 1.2.1.10, to homogeneity in a 5-step chromatographic procedure
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Ni2+-NTA column chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis of the gene nahM from the naphthalene catabolic plasmid pWW60-22 of strain NCIMB9816, gene nahM is organized in the nahNLOMK operon of nahOH genes, genetic organization analysis, overview, overexpression in Escherichia coli strain BL21(DE3) using different plasmid vectors, overview
expressed in Escherichia coli
expressed in Escherichia coli BL21(lambdaDE3)
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expressed in Escherichia coli strain BL21
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gene dmpG encodes the enzyme in the dmp operon together with aldehyde dehydrogenase, EC 1.2.1.10, with which it forms an enzyme complex
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H20A
-
decrease in kcat/Km value
H20S
-
decrease in kcat/Km value
L87A
-
3-fold reduction in kcat/Km
L87A/L89A
-
improved specificity for aldehydes at least four carbons in length
L89A
-
kcat/Km similar to wild type
R16A
-
no detectable activity
R16K
-
increased Km value for 4-hydroxy-2-oxopentanoate
Y290F
-
lower kcat value
Y290S
-
lower kcat value
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