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Literature summary extracted from

  • Kawakami, R.; Noguchi, C.; Higashi, M.; Sakuraba, H.; Ohshima, T.
    Comparative analysis of the catalytic components in the archaeal dye-linked L-proline dehydrogenase complexes (2013), Appl. Microbiol. Biotechnol., 97, 3419-3427 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.5.5.2 sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIPL Thermococcus profundus
1.5.5.2 sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIPL Pyrococcus horikoshii
1.5.5.2 sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIPL Pyrococcus furiosus
1.5.5.2 sequence comparisons and phylogenetic analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus(DE3)-RIPL Thermococcus kodakarensis

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.5.5.2 L-proline substrate inhibition at high L-proline concentrations; substrate inhibition at high L-proline concentrations Pyrococcus furiosus
1.5.5.2 L-proline substrate inhibition at high L-proline concentrations; substrate inhibition at high L-proline concentrations Pyrococcus horikoshii
1.5.5.2 L-proline substrate inhibition at high L-proline concentrations; substrate inhibition at high L-proline concentrations Thermococcus kodakarensis
1.5.5.2 L-proline substrate inhibition at high L-proline concentrations Thermococcus profundus
1.5.5.2 pyrrolidone-5-carboxylate
-
 Pyrococcus furiosus
1.5.5.2 pyrrolidone-5-carboxylate
-
 Pyrococcus horikoshii
1.5.5.2 pyrrolidone-5-carboxylate
-
 Thermococcus kodakarensis
1.5.5.2 pyrrolidone-5-carboxylate
-
 Thermococcus profundus

Organism

EC Number Organism UniProt Comment Textmining
1.5.5.2 Pyrococcus furiosus Q8U022
-
-
1.5.5.2 Pyrococcus furiosus Q8U1G2
-
-
1.5.5.2 Pyrococcus horikoshii O59089
-
-
1.5.5.2 Pyrococcus horikoshii O59445
-
-
1.5.5.2 Pyrococcus horikoshii OT-3 O59089
-
-
1.5.5.2 Pyrococcus horikoshii OT-3 O59445
-
-
1.5.5.2 Thermococcus kodakarensis Q5JFG2
-
-
1.5.5.2 Thermococcus kodakarensis Q5JFG7
-
-
1.5.5.2 Thermococcus kodakarensis KOD1 JCM12380 Q5JFG7
-
-
1.5.5.2 Thermococcus profundus Q76M73
-
-
1.5.5.2 Thermococcus profundus DSM 9503 Q76M73
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.5.5.2 recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Thermococcus profundus
1.5.5.2 recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Pyrococcus furiosus
1.5.5.2 recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Thermococcus kodakarensis
1.5.5.2 recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity, the PH1751 protein tends to aggregate during dialysis Pyrococcus horikoshii

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Thermococcus profundus (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Pyrococcus horikoshii (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Pyrococcus furiosus (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Thermococcus kodakarensis (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Thermococcus kodakarensis KOD1 JCM12380 (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Thermococcus profundus DSM 9503 (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 L-proline + 2,6-dichlorphenol-indophenol
-
 Pyrococcus horikoshii OT-3 (S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorphenol-indophenol
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Thermococcus profundus ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Pyrococcus horikoshii ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Pyrococcus furiosus ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Thermococcus kodakarensis ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Thermococcus kodakarensis KOD1 JCM12380 ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Thermococcus profundus DSM 9503 ?
-
 ?
1.5.5.2 additional information no activity with D-proline, L-hydroxyproline, pyrrolidone-5-carboxylate, sarcosine, and glycine Pyrococcus horikoshii OT-3 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
1.5.5.2 octamer the enzyme is a alpha4beta4-type ProDH Pyrococcus horikoshii
1.5.5.2 octamer the enzyme is a alpha4beta4-type ProDH Pyrococcus furiosus
1.5.5.2 octamer the enzyme is a alpha4beta4-type ProDH Thermococcus kodakarensis
1.5.5.2 tetramer the enzyme is a alphabetagammadelta-type ProDH Thermococcus profundus
1.5.5.2 tetramer the enzyme is a alphabetagammadelta-type ProDH Thermococcus kodakarensis
1.5.5.2 tetramer the enzyme is a alphabetagammadelta-type ProDH Pyrococcus horikoshii
1.5.5.2 tetramer the enzyme is a alphabetagammadelta-type ProDH Pyrococcus furiosus

Synonyms

EC Number Synonyms Comment Organism
1.5.5.2 L-proline dehydrogenase
-
 Thermococcus profundus
1.5.5.2 L-proline dehydrogenase
-
 Pyrococcus horikoshii
1.5.5.2 L-proline dehydrogenase
-
 Pyrococcus furiosus
1.5.5.2 L-proline dehydrogenase
-
 Thermococcus kodakarensis
1.5.5.2 PdhB
-
 Thermococcus profundus
1.5.5.2 PdhB
-
 Thermococcus kodakarensis
1.5.5.2 PDHbeta
-
 Pyrococcus horikoshii
1.5.5.2 PDHbeta
-
 Pyrococcus furiosus
1.5.5.2 PDHbeta
-
 Thermococcus kodakarensis
1.5.5.2 PF1246
-
 Pyrococcus furiosus
1.5.5.2 PF1798
-
 Pyrococcus furiosus
1.5.5.2 PH1364
-
 Pyrococcus horikoshii
1.5.5.2 PH1751
-
 Pyrococcus horikoshii
1.5.5.2 proDH-B1
-
 Pyrococcus horikoshii
1.5.5.2 proDH-B2
-
 Pyrococcus horikoshii
1.5.5.2 TK0117
-
 Thermococcus kodakarensis
1.5.5.2 TK0122
-
 Thermococcus kodakarensis
1.5.5.2 TPpdhbeta
-
 Thermococcus profundus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.5.5.2 50
-
 assay at Thermococcus profundus
1.5.5.2 50
-
 assay at Pyrococcus horikoshii
1.5.5.2 50
-
 assay at Pyrococcus furiosus
1.5.5.2 50
-
 assay at Thermococcus kodakarensis

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.5.5.2 70
-
 the alpha4beta4-type PDHbeta retains more than 80% of its activity after heating at 70°C for 20 min Pyrococcus horikoshii
1.5.5.2 70
-
 the alpha4beta4-type PDHbeta retains more than 80% of its activity after heating at 70°C for 20 min Pyrococcus furiosus
1.5.5.2 70
-
 the alpha4beta4-type PDHbeta retains more than 80% of its activity after heating at 70°C for 20 min Thermococcus kodakarensis
1.5.5.2 70
-
 the alphabetagammadelta-type PDHbeta nearly loses all of its activity during incubation at 70°C for 20 min Pyrococcus horikoshii
1.5.5.2 70
-
 the alphabetagammadelta-type PDHbeta retains 100% of activity during incubation at 70°C for 20 min Pyrococcus furiosus
1.5.5.2 70
-
 the alphabetagammadelta-type PDHbeta retains 68% of activity during incubation at 70°C for 20 min Thermococcus profundus
1.5.5.2 70
-
 the alphabetagammadelta-type PDHbeta retains 76% of activity during incubation at 70°C for 20 min Thermococcus kodakarensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.5.5.2 8
-
 assay at Thermococcus profundus
1.5.5.2 8
-
 assay at Pyrococcus horikoshii
1.5.5.2 8
-
 assay at Pyrococcus furiosus
1.5.5.2 8
-
 assay at Thermococcus kodakarensis

Cofactor

EC Number Cofactor Comment Organism Structure
1.5.5.2 FAD non-covalent binding Thermococcus profundus
1.5.5.2 FAD non-covalent binding Pyrococcus horikoshii
1.5.5.2 FAD non-covalent binding Pyrococcus furiosus
1.5.5.2 FAD non-covalent binding Thermococcus kodakarensis

General Information

EC Number General Information Comment Organism
1.5.5.2 evolution nearly all of the residues responsible for the interaction with substrate and FAD are highly conserved in Pyrococcus and Thermococcus. Phylogenetic analysis shows that the divergence of the alphabetagammadelta-type PDHbetas is spread wider than that of alpha4beta4-type PDHbetas Thermococcus profundus
1.5.5.2 evolution nearly all of the residues responsible for the interaction with substrate and FAD are highly conserved in Pyrococcus and Thermococcus. Phylogenetic analysis shows that the divergence of the alphabetagammadelta-type PDHbetas is spread wider than that of alpha4beta4-type PDHbetas Pyrococcus horikoshii
1.5.5.2 evolution nearly all of the residues responsible for the interaction with substrate and FAD are highly conserved in Pyrococcus and Thermococcus. Phylogenetic analysis shows that the divergence of the alphabetagammadelta-type PDHbetas is spread wider than that of alpha4beta4-type PDHbetas Pyrococcus furiosus
1.5.5.2 evolution nearly all of the residues responsible for the interaction with substrate and FAD are highly conserved in Pyrococcus and Thermococcus. Phylogenetic analysis shows that the divergence of the alphabetagammadelta-type PDHbetas is spread wider than that of alpha4beta4-type PDHbetas Thermococcus kodakarensis
1.5.5.2 additional information values for kcat, Km, and Ki values for L-proline and Ki' for pyrrolidone-5-carboxylate differ greatly among the PDHbeta enzymes, which is in contrast to the optimal temperature and thermostability, and indicates that the kinetic parameters of the PDHbetas are not a reflection of whether the protein is a subunit of an alphabetagammadelta-type PDHbeta or alpha4beta4-type PDHbeta ProDH complex Thermococcus profundus
1.5.5.2 additional information values for kcat, Km, and Ki values for L-proline and Ki' for pyrrolidone-5-carboxylate differ greatly among the PDHbeta enzymes, which is in contrast to the optimal temperature and thermostability, and indicates that the kinetic parameters of the PDHbetas are not a reflection of whether the protein is a subunit of an alphabetagammadelta-type PDHbeta or alpha4beta4-type PDHbeta ProDH complex Pyrococcus horikoshii
1.5.5.2 additional information values for kcat, Km, and Ki values for L-proline and Ki' for pyrrolidone-5-carboxylate differ greatly among the PDHbeta enzymes, which is in contrast to the optimal temperature and thermostability, and indicates that the kinetic parameters of the PDHbetas are not a reflection of whether the protein is a subunit of an alphabetagammadelta-type PDHbeta or alpha4beta4-type PDHbeta ProDH complex Pyrococcus furiosus
1.5.5.2 additional information values for kcat, Km, and Ki values for L-proline and Ki' for pyrrolidone-5-carboxylate differ greatly among the PDHbeta enzymes, which is in contrast to the optimal temperature and thermostability, and indicates that the kinetic parameters of the PDHbetas are not a reflection of whether the protein is a subunit of an alphabetagammadelta-type PDHbeta or alpha4beta4-type PDHbeta ProDH complex Thermococcus kodakarensis