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Literature summary extracted from

  • Soriano, E.V.; McCloskey, D.E.; Kinsland, C.; Pegg, A.E.; Ealick, S.E.
    Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii (2008), Acta Crystallogr. Sect. D, 64, 377-382.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.1.19 Escherichia coli strain MachI is used as a recipient for transformations during plasmid construction and for plasmid propagation and storage. Site-directed mutagenesis is performed on pPRDC.19. The mutant plasmids are transformed into Escherichia coli B834 (DE3) competent cells. Methanocaldococcus jannaschii

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.1.19 the N47A and E109Q mutant proteins are co-crystallized at 22°C with 1-2 mM arginine, the hanging-drop vapor-diffusion method is used. Crystals are grown in 17-20% PEG 2000, 10% 2-methyl-2,4-pentanediol, 2.5% glycerol, 100 mM HEPES pH 6.7-7.3, 0.5 mM beta-octylglucoside, 0.5 mM ethylenediaminetetraacetic acid and 10 mM dithiothreitol. Methanocaldococcus jannaschii

Protein Variants

EC Number Protein Variants Comment Organism
4.1.1.19 E109Q E109Q mutation reduces the activity by 7.7fold compared to the wild type enzyme, reduced decarboxylation activity results in part from incomplete pyruvoyl-group formation Methanocaldococcus jannaschii
4.1.1.19 N47A The activity of N47A is reduced by 500fold compared with the wild type protein Methanocaldococcus jannaschii

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.1.19 L-arginine Methanocaldococcus jannaschii enzyme catalyzes the first step of the polyamine-biosynthetic pathway agmatine + CO2
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 ?

Organism

EC Number Organism UniProt Comment Textmining
4.1.1.19 Methanocaldococcus jannaschii Q57764
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Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.1.19 purification and cleavage of the N-terminal His-tag are performed Methanocaldococcus jannaschii

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
4.1.1.19 0.002
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 murtant N47A, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine Methanocaldococcus jannaschii
4.1.1.19 0.132
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 mutant E109Q, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine Methanocaldococcus jannaschii
4.1.1.19 1.014
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 wild type enzyme, assay is carried out in 50 mM 2-(N-morpholino)ethanesulfonic acid/NaOH buffer, 50 mM KCl, 1 mM DTT with 4 mM L-arginine and 2 microl [14C] L-arginine Methanocaldococcus jannaschii

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.1.19 L-arginine enzyme catalyzes the first step of the polyamine-biosynthetic pathway Methanocaldococcus jannaschii agmatine + CO2
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 ?

Subunits

EC Number Subunits Comment Organism
4.1.1.19 trimer Mutant E109Q, the structure contains 2 complete trimers in the asymmetric unit, the active sites of each trimer are located between adjacent protomers. All 6 protomers are fully processed and contain the product agmatine at the active site. The presence of the product agmatine confirms that the mutant is active because the substrate arginine is added to the protein during crystallization. Methanocaldococcus jannaschii
4.1.1.19 trimer Mutant N47A, the structure contains 2 complete trimers in the asymmetric unit, the active sites of each trimer are located between adjacent protomers. The mutant protein does not show complete processing in all protomers. The first protomer of N47A is processed showing clear cleavage of the protomer to form the beta-chain (residues 1-52) and the alpha-chain (residues 53-165). A second protomer is unprocessed, showing clear density connecting residues Ser52 and Ser53. The final protomer in the first trimer can not easily be classified as either processed or unprocessed and is likely to be a mixture of the two states. The density between Ser52 and Ser53 is weak, density is also present corresponding to the pyruvoyl group and the product agmatine. Methanocaldococcus jannaschii

Synonyms

EC Number Synonyms Comment Organism
4.1.1.19 arginine decarboxylase
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 Methanocaldococcus jannaschii
4.1.1.19 PvlArgDC
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 Methanocaldococcus jannaschii
4.1.1.19 pyruvoyl-dependent arginine decarboxylase
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 Methanocaldococcus jannaschii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.1.19 70
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 assay at Methanocaldococcus jannaschii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.1.19 6
-
 assay at Methanocaldococcus jannaschii

Cofactor

EC Number Cofactor Comment Organism Structure
4.1.1.19 additional information the enzyme contains a reactive pyruvoyl group, the proenzyme undergoes autocatalytic serinolysis, resulting in the formation of two chains and the creation of a pyruvoyl group, which is the cofactor for the decarboxylation reaction Methanocaldococcus jannaschii