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Literature summary for 4.1.1.9 extracted from

  • Froese, D.S.; Forouhar, F.; Tran, T.H.; Vollmar, M.; Kim, Y.S.; Lew, S.; Neely, H.; Seetharaman, J.; Shen, Y.; Xiao, R.; Acton, T.B.; Everett, J.K.; Cannone, G.; Puranik, S.; Savitsky, P.; Krojer, T.; Pilka, E.S.; Kiyani, W.; Lee, W.H.; Marsden, B.D.; von Delft, F.; Allerston, C.K.; Spagnolo, L.; Gileadi, O.; , M.
    Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations (2013), Structure, 21, 1182-1192.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

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

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

Localization Comment Organism GeneOntology No. Textmining
cytoplasm
-
Homo sapiens 5737
-
mitochondrion
-
Homo sapiens 5739
-
peroxisome
-
Homo sapiens 5777
-

Organism

Organism UniProt Comment Textmining
Agrobacterium vitis B9K0V9
-
-
Cupriavidus metallidurans Q1LJK6
-
-
Cupriavidus metallidurans CH34 Q1LJK6
-
-
Homo sapiens O95822
-
-
Rhodopseudomonas palustris
-
-
-

Substrates and Products (Substrate)

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

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

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

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

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