Crystallization (Comment) | Organism |
---|---|
purified recombinant enzyme, microbatch method, 0.002 ml of the protein solution containing 10 mM Tris, pH 7.5, 100 mM NaCl, 5 mM DTT, and 0.02% NaN3 are mixed with 0.002 ml of the precipitant solution consisting of 0.1 M magnesium nitrate, 100 mM Tris, pH 8.5, and 33% v/v PEG 400, 18°C, X-ray diffraction structure determination and analysis at 2.3-3.1 A, selenomethionyl single-wavelength anomalous diffraction method, molecular replacement | Rhodopseudomonas palustris |
purified recombinant enzyme, microbatch method, 0.002 ml of the protein solution containing 10 mM Tris, pH 7.5, 100 mM NaCl, 5 mM DTT, and 0.02% NaN3 are mixed with 0.002 ml of the precipitant solution consisting of 200 mM ammonium sulfate, and 20% w/v PEG3350, 18°C, X-ray diffraction structure determination and analysis at 2.3-3.1 A, selenomethionyl single-wavelength anomalous diffraction method, molecular replacement | Agrobacterium vitis |
purified recombinant enzyme, microbatch method, mixingof 0.002 ml of protein in 20 mM Tris, pH 7.0, 250 mM NaCl, 5% v/v glycerol, and 3 mM malonyl-CoA with crystallization solution containing 160 mM magnesium chloride, 80 mM Tris, pH 8.5, 24% w/v PEG 4000, 20% v/v glycerol, and 3% v/v ethanol, 18°C, X-ray diffraction structure determination and analysis at 2.3-3.1 A, selenomethionyl single-wavelength anomalous diffraction method, molecular replacement | Cupriavidus metallidurans |
recombinant mutant E58A/K59A/E278A/E279A/K280A, sitting-drop vapor diffusion method, mixing of 10 mg/ml protein in HEPES, pH 7.5, 100 mM NaCl, 1% v/v glycerol, and 5 mM decanoyl-CoA. in a 2:1 ratio with a precipitant solution containing 10% w/v PEG 20000 and 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.0, at room temperature, X-ray diffraction structure determination and analysis at 2.8 A, by single isomorphous replacement with anomalous scattering | Homo sapiens |
Protein Variants | Comment | Organism |
---|---|---|
A69V | naturally occuring mutation in the N-terminal helical domain, the mutantion is involved in enzyme deficiency | Homo sapiens |
E58A/K59A/E278A/E279A/K280A | site-directed mutagenesis, crystal structure determination. The mutant exhibits similar oligomeric and enzymatic properties as wild-typ, both alanine-substituted patches are located in surface-exposed regions: Glu58-Lys59 is found in the loop connecting helices alphaA and alphaB, while the loop containing residues 278-280, connecting strands beta3 and beta4, is disordered | Homo sapiens |
G300V | naturally occuring mutation in the GNAT core, the mutantion is involved in enzyme deficiency | Homo sapiens |
H423N | site-directed mutagenesis, the mutant shows a 7fold loss in kcat compared to the wild-type enzyme | Homo sapiens |
L161P | naturally occuring mutation in the N-terminal helical domain, the mutantion is involved in enzyme deficiency | Homo sapiens |
L307R | naturally occuring mutation in the GNAT core, the mutantion is involved in enzyme deficiency | Homo sapiens |
S290F | naturally occuring mutation in the GNAT core, the mutantion is involved in enzyme deficiency | Homo sapiens |
S290F | site-directed mutagenesis, the mutant shows a 2fold decrease in kcat in vitro compared to the wild-type enzyme | Homo sapiens |
S329A | site-directed mutagenesis, the mutant shows a 110fold loss in kcat and 58fold loss in kcat/Km compared to the wild-type enzyme | Homo sapiens |
S440I | naturally occuring mutation in the catalytic domain, the mutantion is involved in enzyme deficiency | Homo sapiens |
S477F | naturally occuring mutation in the catalytic domain, the mutantion is involved in enzyme deficiency | Homo sapiens |
W384C | naturally occuring mutation in the catalytic domain, the mutantion is involved in enzyme deficiency | Homo sapiens |
Y456S | naturally occuring mutation in the GNAT core, the mutantion is involved in enzyme deficiency | Homo sapiens |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
cytoplasm | - |
Homo sapiens | 5737 | - |
mitochondrion | - |
Homo sapiens | 5739 | - |
peroxisome | - |
Homo sapiens | 5777 | - |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Agrobacterium vitis | B9K0V9 | - |
- |
Cupriavidus metallidurans | Q1LJK6 | - |
- |
Cupriavidus metallidurans CH34 | Q1LJK6 | - |
- |
Homo sapiens | O95822 | - |
- |
Rhodopseudomonas palustris | - |
- |
- |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
Malonyl-CoA | - |
Rhodopseudomonas palustris | Acetyl-CoA + CO2 | - |
? | |
Malonyl-CoA | - |
Homo sapiens | Acetyl-CoA + CO2 | - |
? | |
Malonyl-CoA | - |
Agrobacterium vitis | Acetyl-CoA + CO2 | - |
? | |
Malonyl-CoA | - |
Cupriavidus metallidurans | Acetyl-CoA + CO2 | - |
? | |
Malonyl-CoA | - |
Cupriavidus metallidurans CH34 | Acetyl-CoA + CO2 | - |
? |
Subunits | Comment | Organism |
---|---|---|
More | organization of the helical domains and the oligomeric states and intersubunit interfaces, secondary sequence comparisons, subunit structure and oligomeric architecture analysis and comparisons, overview. The MCD monomer contains an N-terminal helical domain and a C-terminal catalytic domain | Rhodopseudomonas palustris |
More | organization of the helical domains and the oligomeric states and intersubunit interfaces, secondary sequence comparisons, subunit structure and oligomeric architecture analysis and comparisons, overview. The MCD monomer contains an N-terminal helical domain and a C-terminal catalytic domain | Homo sapiens |
More | organization of the helical domains and the oligomeric states and intersubunit interfaces, secondary sequence comparisons, subunit structure and oligomeric architecture analysis and comparisons, overview. The MCD monomer contains an N-terminal helical domain and a C-terminal catalytic domain | Agrobacterium vitis |
More | organization of the helical domains and the oligomeric states and intersubunit interfaces, secondary sequence comparisons, subunit structure and oligomeric architecture analysis and comparisons, overview. The MCD monomer contains an N-terminal helical domain and a C-terminal catalytic domain | Cupriavidus metallidurans |
Synonyms | Comment | Organism |
---|---|---|
malonyl-coenzyme A decarboxylase | - |
Rhodopseudomonas palustris |
malonyl-coenzyme A decarboxylase | - |
Homo sapiens |
malonyl-coenzyme A decarboxylase | - |
Agrobacterium vitis |
malonyl-coenzyme A decarboxylase | - |
Cupriavidus metallidurans |
MCD | - |
Rhodopseudomonas palustris |
MCD | - |
Homo sapiens |
MCD | - |
Agrobacterium vitis |
MCD | - |
Cupriavidus metallidurans |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Rhodopseudomonas palustris |
7.5 | - |
assay at | Homo sapiens |
7.5 | - |
assay at | Agrobacterium vitis |
7.5 | - |
assay at | Cupriavidus metallidurans |
General Information | Comment | Organism |
---|---|---|
evolution | the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis | Rhodopseudomonas palustris |
evolution | the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis | Homo sapiens |
evolution | the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis | Agrobacterium vitis |
evolution | the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis | Cupriavidus metallidurans |
malfunction | impact of loss-of-function alleles in hereditary MCD deficiency | Homo sapiens |
additional information | catalytic domain structure and active site structure comparisons, overview | Rhodopseudomonas palustris |
additional information | catalytic domain structure and active site structure comparisons, overview | Agrobacterium vitis |
additional information | catalytic domain structure and active site structure comparisons, overview | Cupriavidus metallidurans |
additional information | catalytic domain structure and active site structure, with His-Ser/Thr dyad, comparisons, overview. The catalytic domain of MCD contains a central eight-stranded, mostly antiparallel etab sheet (beta1-beta8) that is surrounded by at least 11 alpha helices. The substrate can position its thioester carbonyl, bridging the carboxylate leaving group and CoA backbone, in the vicinity of Ser329 and His423 | Homo sapiens |