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Literature summary for 4.1.3.24 extracted from
- The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases (2013), BMC Struct. Biol., 13, 28.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| phylogenetic analysis, recombinant expression in Escherichia coli | Chloroflexus aurantiacus |
| phylogenetic analysis, recombinant expression of His10-tagged enzyme in Escherichia coli | Cereibacter sphaeroides |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| 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 | Chloroflexus aurantiacus |
| 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 | Cereibacter sphaeroides |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| oxalate | - |
Cereibacter sphaeroides |  |
| oxalate | - |
Chloroflexus aurantiacus | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required, binding structure, coordination by Glu141 and Asp168, overview | Cereibacter sphaeroides | |
| Mg2+ | required, binding structure, coordination by Glu157 and Asp184, overview | Chloroflexus aurantiacus | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 36800 | - |
6 * 36800, 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 | Cereibacter sphaeroides |
| 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 | Chloroflexus aurantiacus |
| 220000 | - |
recombinant His10-tagged enzyme, gel filtration | Cereibacter sphaeroides |
| 228000 | - |
recombinant enzyme, gel filtration | Chloroflexus aurantiacus |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (2R,3S)-2-methylmalyl-CoA | Cereibacter sphaeroides | - |
propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | Chloroflexus aurantiacus | - |
propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | Chloroflexus aurantiacus OK-70-fl / DSM 636 | - |
propanoyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | Cereibacter sphaeroides | - |
acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | Chloroflexus aurantiacus | - |
acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | Chloroflexus aurantiacus OK-70-fl / DSM 636 | - |
acetyl-CoA + glyoxylate | - |
r | |
| additional information | Cereibacter sphaeroides | malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters | ? | - |
? | |
| additional information | Chloroflexus aurantiacus | 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 | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Cereibacter sphaeroides | Q3J5L6 | - |
- |
| Chloroflexus aurantiacus | S5N020 | - |
- |
| Chloroflexus aurantiacus OK-70-fl / DSM 636 | S5N020 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli | Chloroflexus aurantiacus |
| recombinant His10-tagged enzyme from Escherichia coli | Cereibacter sphaeroides |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (2R,3S)-2-methylmalyl-CoA | - |
Cereibacter sphaeroides | propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | - |
Chloroflexus aurantiacus | propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | the synthesis direction is preferred | Cereibacter sphaeroides | propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | the synthesis direction is preferred | Chloroflexus aurantiacus | propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | - |
Chloroflexus aurantiacus OK-70-fl / DSM 636 | propanoyl-CoA + glyoxylate | - |
r | |
| (2R,3S)-2-methylmalyl-CoA | the synthesis direction is preferred | Chloroflexus aurantiacus OK-70-fl / DSM 636 | propanoyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | - |
Cereibacter sphaeroides | acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | - |
Chloroflexus aurantiacus | acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | the cleavage direction is preferred | Cereibacter sphaeroides | acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | the cleavage direction is preferred | Chloroflexus aurantiacus | acetyl-CoA + glyoxylate | - |
r | |
| (S)-malyl-CoA | - |
Chloroflexus aurantiacus OK-70-fl / DSM 636 | acetyl-CoA + glyoxylate | - |
r | |
| additional information | malyl-CoA lyase is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related CoA thioesters | Cereibacter sphaeroides | ? | - |
? | |
| 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 | Chloroflexus aurantiacus | ? | - |
? | |
| additional information | modeling of binding structures of glyoxylate, acetyl-CoA, pyruvate, and Mg2+, overview | Cereibacter sphaeroides | ? | - |
? | |
| 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 | Chloroflexus aurantiacus | ? | - |
? | |
| 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 | Chloroflexus aurantiacus OK-70-fl / DSM 636 | ? | - |
? | |
| 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 | Chloroflexus aurantiacus OK-70-fl / DSM 636 | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| hexamer | 6 * 36800, 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 | Cereibacter sphaeroides |
| hexamer | 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 | Chloroflexus aurantiacus |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| L-malyl-CoA/beta-methylmalyl-CoA lyase | UniProt | Cereibacter sphaeroides |
| malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase | UniProt | Chloroflexus aurantiacus |
| MCL | - |
Cereibacter sphaeroides |
| MCL | - |
Chloroflexus aurantiacus |
| MCLC | - |
Chloroflexus aurantiacus |
| MCLR | - |
Cereibacter sphaeroides |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the large superfamily of CitE-like enzymes, which includes the beta-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases) | Cereibacter sphaeroides |
| evolution | the enzyme belongs to the large superfamily of CitE-like enzymes, which includes the beta-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases) | Chloroflexus aurantiacus |
| metabolism | the enzyme belongs to a group of organisms that lack isocitrate lyase. Therefore, they are unable to use the glyoxylate bypass to assimilate acetyl-CoA or other substrates that enter central carbon metabolism at the level of acetyl-CoA. Instead, they use the ethylmalonyl-CoA pathway for the assimilation of acetyl-CoA with the bifunctional enzyme catalyzing the cleavage of beta-methylmalyl-CoA and the synthesis of malyl-CoA | Cereibacter sphaeroides |
| metabolism | the enzyme catalyzes three different steps in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation, the tri-functionality of the MCLC underscores its key role for this pathway | Chloroflexus aurantiacus |
| additional information | upon ligand binding, changes in the C-terminal domains of the enzyme results in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer, overview | Cereibacter sphaeroides |
| additional information | upon ligand binding, changes in the C-terminal domains of the enzyme results in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer, overview | Chloroflexus aurantiacus |
| physiological function | the enzyme from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation | Cereibacter sphaeroides |
| physiological function | the enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus | Chloroflexus aurantiacus |
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