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Information on EC 4.1.3.24 - malyl-CoA lyase
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4.1.3.24 malyl-CoA lyaseIUBMB Comments
The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation . 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].
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Word Map
- 4.1.3.24
- malate
-
methylobacterium
- extorquens
-
facultative
- 3-hydroxypropionate
- methanol
- carboxylase
- propionyl-coa
- sphaeroides
-
chloroflexus
- phosphoenolpyruvate
-
rhodobacter
-
phototrophic
- aurantiacus
- ethylmalonyl-coa
- hydroxypyruvate
-
one-carbon
- thioesters
-
acetyl-coenzyme
- ribulose
- succinyl-coa
- lyases
-
carbon-carbon
-
roseiflexus
-
succinate-grown
-
multicarbon
- 3-hydroxybutyrate
-
calvin
-
condenses
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Reaction Schemes
Synonyms
malyl-coa lyase, l-malyl-coa lyase/beta-methylmalyl-coa lyase, malyl coenzyme a lyase, malyl-coa/beta-methylmalyl-coa lyase, (3s)-malyl-coa lyase, l-malyl-coa/beta-methylmalyl-coa lyase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
L-malyl-CoA lyase/beta-methylmalyl-CoA lyase
-
the two enzymes are identical and both enzymatic reactions are catalysed by one single bifunctional enzyme
lyase, malyl coenzyme A
-
-
-
-
malyl coenzyme A lyase
-
-
-
-
malyl-CoA/beta-methylmalyl-CoA lyase
malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase
MCL
MCLC
malyl-CoA/beta-methylmalyl-CoA lyase
Methylorubrum extorquens ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1
-
protein MclA2
-
malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase
Chloroflexus aurantiacus OK-70-fl / DSM 636
UniProt
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
(2)
-
-
-
(S)-malyl-CoA = acetyl-CoA + glyoxylate
in the reverse direction ordered sequential mechanism with glyoxylate binding prior to acetyl-CoA
-
(S)-malyl-CoA = acetyl-CoA + glyoxylate
(1)
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
elimination
-
-
of an oxo-acid, C-C bond cleavage
-
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PATHWAY SOURCE
PATHWAYS
KEGG
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SYSTEMATIC NAME
IUBMB Comments
(S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation [6]. 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].
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CAS REGISTRY NUMBER
COMMENTARY
37290-67-8
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
propionyl-CoA + glyoxylate
(2S)-4-(beta-methyl)-malyl-CoA
-
-
-
r
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
the synthesis direction is preferred
-
-
r
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
the synthesis direction is preferred
-
-
r
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
-
-
-
r
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
the synthesis direction is preferred
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
malyl-CoA
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
enzyme in 3-hydroxypropionate cycle
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
-
enzyme in 3-hydroxypropionate cycle
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Methylobacterium hypolimneticum
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Methylobacterium methanolicum
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Pseudomonas methanolica
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
?
(S)-malyl-CoA
acetyl-CoA + glyoxylate
the cleavage direction is preferred
-
-
r
(S)-malyl-CoA
acetyl-CoA + glyoxylate
the cleavage direction is preferred
-
-
r
acetyl-CoA + glyoxylate
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
-
-
-
r
acetyl-CoA + glyoxylate
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
-
-
-
r
beta-methylmalyl-CoA
glyoxylate + propionyl-CoA
Methylorubrum extorquens ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1
-
-
-
-
?
propionyl-CoA + glyoxylate
erythro-beta-methylmalyl-CoA
-
-
-
?
additional information
?
-
malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
-
malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
modeling of binding structures of glyoxylate, acetyl-CoA, pyruvate, and Mg2+, overview
-
-
?
additional information
?
-
-
modeling of binding structures of glyoxylate, acetyl-CoA, pyruvate, and Mg2+, overview
-
-
?
additional information
?
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25
-
-
?
additional information
?
-
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25
-
-
?
additional information
?
-
Chloroflexus aurantiacus OK-70-fl / DSM 636
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
Chloroflexus aurantiacus OK-70-fl / DSM 636
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the enzyme may serve as a route to Gly during biosynthesis of purines and proteins
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
Pseudomonas methanolica
-
the enzyme may serve as a route to Gly during biosynthesis of purines and proteins
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
propionyl-CoA + glyoxylate
(2S)-4-(beta-methyl)-malyl-CoA
-
-
-
r
(2R,3S)-2-methylmalyl-CoA
propanoyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
-
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
-
-
r
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
-
enzyme in 3-hydroxypropionate cycle
-
?
(3S)-3-carboxy-3-hydroxypropanoyl-CoA
acetyl-CoA + glyoxylate
Chloroflexus aurantiacus OK-70-fl / DSM 636
-
enzyme in 3-hydroxypropionate cycle
-
?
additional information
?
-
malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
-
malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
-
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
Chloroflexus aurantiacus OK-70-fl / DSM 636
the enzyme also catalzes the reversible cleavage of (S)-citramalyl-CoA to acetyl-CoA and pyruvate, reaction of EC 4.1.3.25. Malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the enzyme may serve as a route to Gly during biosynthesis of purines and proteins
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
-
the role in C1 metabolism, in organisms utilizing the Ser pathway, may be to provide the glyoxylate necessary to sustain operations of this pathway
-
-
?
additional information
?
-
Pseudomonas methanolica
-
the enzyme may serve as a route to Gly during biosynthesis of purines and proteins
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
additional information
?
-
-
the specific activity of malyl-CoA lyase is severalfold higher when grown on C1 compounds than when grown on C2, C3 or C4 compounds
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mg2+
Mn2+
Zn2+
-
divalent cation required, 41% of the activation with Mg2+ and Co2+
Mg2+
required, binding structure, coordination by Glu141 and Asp168, overview
Mg2+
required, binding structure, coordination by Glu157 and Asp184, overview
Mg2+
-
divalent cation required, Mg2+ or Co2+ is most effective
Mn2+
-
divalent cation required, 88% of the activation with Mg2+ and Co2+
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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
acetyl-CoA
-
in direction of malyl-CoA cleavage: noncompetitive with respect to malyl-CoA
oxalate
-
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
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
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
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3.1
glyoxylate
condensation of acetyl-CoA and glyoxylate, at 30°C
4.1
glyoxylate
condensation of propionyl-CoA and glyoxylate, at 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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