Information on EC 4.1.3.24 - malyl-CoA lyase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.3.24
-
RECOMMENDED NAME
GeneOntology No.
malyl-CoA lyase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
show the reaction diagram
(2)
-
-
-
(S)-malyl-CoA = acetyl-CoA + glyoxylate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
of an oxo-acid, C-C bond cleavage
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3-hydroxypropanoate cycle
-
-
C5-Branched dibasic acid metabolism
-
-
Carbon fixation pathways in prokaryotes
-
-
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)
-
-
ethylmalonyl-CoA pathway
-
-
formaldehyde assimilation I (serine pathway)
-
-
Glyoxylate and dicarboxylate metabolism
-
-
glyoxylate assimilation
-
-
Methane metabolism
-
-
methylaspartate cycle
-
-
Microbial metabolism in diverse environments
-
-
ethylmalonyl-CoA pathway
-
-
SYSTEMATIC NAME
IUBMB Comments
(S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4]. The enzymes from Rhodobacter species are part of acetate assimilation pathways [3,5]. The reactions are reversible.
CAS REGISTRY NUMBER
COMMENTARY hide
37290-67-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain X
-
-
Manually annotated by BRENDA team
strain X
-
-
Manually annotated by BRENDA team
Methylobacterium hypolimneticum
-
-
-
Manually annotated by BRENDA team
Methylobacterium methanolicum
-
-
-
Manually annotated by BRENDA team
Pseudomonas methanolica
-
-
-
Manually annotated by BRENDA team
strain MA
-
-
Manually annotated by BRENDA team
strain MS
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
show the reaction diagram
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
show the reaction diagram
(3S)-malyl-CoA
acetyl-CoA + glyoxylate
show the reaction diagram
-
-
-
r
(S)-malyl-CoA
acetyl-CoA + glyoxylate
show the reaction diagram
acetyl-CoA + glyoxylate
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
show the reaction diagram
acetyl-CoA + glyoxylate
L-malyl-CoA
show the reaction diagram
-
-
-
-
r
beta-methylmalyl-CoA
glyoxylate + propionyl-CoA
show the reaction diagram
propionyl-CoA + glyoxylate
erythro-beta-methylmalyl-CoA
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
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
show the reaction diagram
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
show the reaction diagram
(S)-malyl-CoA
acetyl-CoA + glyoxylate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
-
divalent cation required, 41% of the activation with Mg2+ and Co2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R)-4-malyl-CoA
-
-
acetyl-CoA
Ca2+
-
14% specific activity at 10 mM
Co2+
-
13% specific activity at 10 mM
glycolate
-
in direction of malyl-CoA synthesis: competitive with respect to glyoxylate and noncompetitive with respect to acetyl-CoA.In direction of malyl-CoA cleavage: competitive with respect to malyl-CoA
Ni2+
-
6% specific activity at 10 mM
oxalate
oxylate
-
in direction of malyl-CoA cleavage: competitive with respect to malyl-CoA
-
propionyl-CoA
-
in direction of malyl-CoA synthesis: uncompetitive with respect to glyoxylate and competitive with respect to acetyl-CoA. In direction of malyl-CoA cleavage: noncompetitive with respect to malyl-CoA
succinate
-
activity is downregulated 10fold
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acetate
-
growth of the mcl1::kan mutant on acetate is not rescued by the addition of glyoxylate, the mutant growth rates are comparable to those of the wild type on substrates downstream of the proposed metabolic block, i.e., malate and propionate plus bicarbonate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.005 - 0.5
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
0.02
(3S)-malyl-CoA
-
at 30°C
0.015 - 0.36
acetyl-CoA
0.01 - 0.089
beta-methylmalyl-CoA
0.021
erythro-beta-methylmalyl-CoA
-
-
0.8 - 4.1
glyoxylate
0.015
malyl-CoA
-
-
0.2 - 1.2
propionyl-CoA
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.8
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
Chloroflexus aurantiacus
-
pH 7.1, 55°C
2.5
(3S)-malyl-CoA
Rhodobacter sphaeroides
-
at 30°C
8.6
acetyl-CoA
Rhodobacter sphaeroides
-
at 30°C
2.8
beta-methylmalyl-CoA
Rhodobacter sphaeroides
-
at 30°C
12
propionyl-CoA
Rhodobacter sphaeroides
-
at 30°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.47
-
-
0.48
-
acetyl-CoA condensation
0.5
-
propionyl-CoA condensation
2.3
-
L-malyl-CoA lyase activity
4.1
-
cleavage of (3S)-malyl-CoA
4.5
-
cleavage of beta-methylmalyl-CoA
5.7
-
cleavage of erythro-beta-methylmalyl-CoA
6.5
-
beta-methylmalyl-CoA lyase activity
14
-
condensation of acetyl-CoA and glyoxylate
18
-
cleavage of L-malyl-CoA
20
-
condensation of propionyl-CoA and glyoxylate
37
-
condensation of acetyl-CoA with glyoxylate
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 10
-
pH 6.5: about 55% of maximal activity, pH 10.0: about 45% of maximal activity
6.6 - 8.3
-
half maximal activity at pH 6.6 and pH 8.3
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
malyl-CoA lyase activity is 20fold upregulated in acetate-grown cells versus glucose-grown cells
Manually annotated by BRENDA team
-
malyl-CoA lyase activity is 20fold upregulated in acetate-grown cells versus glucose-grown cells
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)
Methylobacterium extorquens (strain DSM 6343 / CIP 106787 / DM4)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35000
-
6 * 35000, SDS-PAGE
38000
-
x * 38000, alpha5 or alpha6, SDS-PAGE
38400
6 * 38400, about, sequence calculation, dimer of trimers, elaborations on the canonical beta8/alpha8 TIM barrel fold and form hexameric assemblies. The trimeric assembly itself is a prerequisite for the catalytic activity
190000
-
meniscus depletion method
195000
-
gel filtration
200000
-
gel filtration
210000
-
gel filtration
220000
-
recombinant His10-tagged enzyme, gel filtration
228000
recombinant enzyme, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
-
x * 38000, alpha5 or alpha6, SDS-PAGE
hexamer
homohexamer
-
4 * 36800, by sequence analysis
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, alone or in complex with substrate propionyl-CoA, inhibitor oxalate, and magnesium ions, pH 5.5, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement modeling
purified recombinant His10-tagged enzyme alone or in complex with substrate propionyl-CoA, inhibitor oxalate, and magnesium ions, pH 7.5, X-ray diffraction structure determination and analysis at 2.5 A resolution, molecular replacement
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
-
irreversible loss of activity
65
-
stable for 20 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, stable for several months
-
-20°C, 10% w/w glycerol, stable for several weeks
-
0-4°C, 2-3 weeks, stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by affinity chromatography
-
recombinant enzyme from Escherichia coli
recombinant His10-tagged enzyme from Escherichia coli
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
-
expression in Escherichia coli
-
into pET16b and expressed as an N-terminal deca-His tag fusion protein in Escherichia coli BL21(DE3) cells
-
phylogenetic analysis, recombinant expression in Escherichia coli
phylogenetic analysis, recombinant expression of His10-tagged enzyme in Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
2.4-fold induction during growth on ethylamine
-
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