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Literature summary for 1.5.5.2 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)

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

Inhibitors

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

Organism

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

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Thermococcus profundus
recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Pyrococcus furiosus
recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus(DE3)-RIPL by nickel affinity chromatography and dialysis to homogeneity Thermococcus kodakarensis
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)

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

Subunits

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

Synonyms

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

Temperature Optimum [°C]

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

Temperature Stability [°C]

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

pH Optimum

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

Cofactor

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

General Information

General Information Comment Organism
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
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
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
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
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
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
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
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