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Literature summary extracted from

  • Fukuyama, S.; Mihara, H.; Miyake, R.; Ueda, M.; Esaki, N.; Kurihara, T.
    Characterization of a thermostable 2,4-diaminopentanoate dehydrogenase from Fervidobacterium nodosum Rt17-B1 (2014), J. Biosci. Bioeng., 117, 551-556 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.4.1.12 expressed in Escherichia coli Rosetta (DE3) cells Fervidobacterium nodosum
1.4.1.26 expressed in Escherichia coli Rosetta (DE3) cells Fervidobacterium nodosum

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.4.1.12 (2R,4S)-2,4-diaminopentanoate uncompetitive substrate inhibition Fervidobacterium nodosum
1.4.1.12 Ca2+ 85% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.12 Co2+ 34% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.12 Cu2+ complete inhibition at 0.5 mM Fervidobacterium nodosum
1.4.1.12 D-ornithine uncompetitive inhibition Fervidobacterium nodosum
1.4.1.12 Fe2+ 84% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.12 Mg2+ 65% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.12 additional information not inhibited by EDTA, KBr, KCl, KNO3, CH3COOK, and K2SO4 Fervidobacterium nodosum
1.4.1.12 Ni2+ 2% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.12 Zn2+ 2% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 (2R, 4S)-2,4-diaminopentanoate uncompetitive substrate inhibition Fervidobacterium nodosum
1.4.1.26 Ca2+ 85% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 Co2+ 34% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 Cu2+ complete inhibition at 0.5 mM Fervidobacterium nodosum
1.4.1.26 D-alanine enzymatic activity decreases to 71% of the positive control at 5 mM Fervidobacterium nodosum
1.4.1.26 D-Lysine enzymatic activity decreases to 68% of the positive control at 5 mM Fervidobacterium nodosum
1.4.1.26 D-ornithine uncompetitive inhibition, enzymatic activity decreases to 14% of the positive control at 5 mM Fervidobacterium nodosum
1.4.1.26 Fe2+ 84% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 Mg2+ 65% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 additional information EDTA does not affect the enzyme activity Fervidobacterium nodosum
1.4.1.26 Ni2+ 2% residual activity at 0.5 mM Fervidobacterium nodosum
1.4.1.26 Zn2+ 2% residual activity at 0.5 mM Fervidobacterium nodosum

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.4.1.12 0.05
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 0.2
-
 (2R,4S)-2,4-diaminopentanoate at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 2
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 2
-
 (2R,5S)-2,5-diaminohexanoate at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 0.05
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 0.2
-
 (2R,4S)-2,4-diaminopentanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 2
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 2
-
 2,5-Diaminohexanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.4.1.12 additional information Mn2+ has no significant effect on enzyme activity Fervidobacterium nodosum
1.4.1.26 additional information K+ and Mn2+ have no significant effect on the enzyme activity Fervidobacterium nodosum

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.4.1.12 (2R,4S)-2,4-diaminopentanoate + H2O + NAD+ Fervidobacterium nodosum
-
 (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
-
 ?
1.4.1.12 (2R,4S)-2,4-diaminopentanoate + H2O + NADP+ Fervidobacterium nodosum
-
 (2R)-2-amino-4-oxopentanoate + NH3 + NADPH + H+
-
 ?
1.4.1.26 (2R,4S)-2,4-diaminopentanoate + H2O + NAD+ Fervidobacterium nodosum
-
 (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
-
 ?
1.4.1.26 (2R,4S)-2,4-diaminopentanoate + H2O + NADP+ Fervidobacterium nodosum
-
 (2R)-2-amino-4-oxopentanoate + NH3 + NADPH + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.4.1.12 Fervidobacterium nodosum
-
-
-
1.4.1.26 Fervidobacterium nodosum
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.4.1.26 His-Bind column chromatography Fervidobacterium nodosum

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
1.4.1.26 1
-
 with 2,5-diaminohexanoate as substrate, at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 92
-
 with (2R,4S)-2,4-diaminopentanoate as substrate, at pH 8.5 and 55°C Fervidobacterium nodosum

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.4.1.12 (2R,4S)-2,4-diaminopentanoate + H2O + NAD+
-
 Fervidobacterium nodosum (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
-
 ?
1.4.1.12 (2R,4S)-2,4-diaminopentanoate + H2O + NADP+
-
 Fervidobacterium nodosum (2R)-2-amino-4-oxopentanoate + NH3 + NADPH + H+
-
 ?
1.4.1.12 (2R,5S)-2,5-diaminohexanoate + H2O + NADP+
-
 Fervidobacterium nodosum (2R)-2-amino-5-oxohexanoate + NH3 + NADPH + H+
-
 ?
1.4.1.26 (2R,4S)-2,4-diaminopentanoate + H2O + NAD+
-
 Fervidobacterium nodosum (2R)-2-amino-4-oxopentanoate + NH3 + NADH + H+
-
 ?
1.4.1.26 (2R,4S)-2,4-diaminopentanoate + H2O + NADP+
-
 Fervidobacterium nodosum (2R)-2-amino-4-oxopentanoate + NH3 + NADPH + H+
-
 ?
1.4.1.26 2,5-diaminohexanoate + H2O + NAD+ 90fold less activity with 2,5-diaminohexanoate compared to (2R,4S)-2,4-diaminopentanoate Fervidobacterium nodosum 2-amino-5-oxohexanoate + NH3 + NADH + H+
-
 ?

Subunits

EC Number Subunits Comment Organism
1.4.1.12 ? x * 38000, SDS-PAGE Fervidobacterium nodosum
1.4.1.26 homodimer 2 * 38000, SDS-PAGE Fervidobacterium nodosum
1.4.1.26 homodimer 2 * 38000, calculated from amino acid sequence Fervidobacterium nodosum

Synonyms

EC Number Synonyms Comment Organism
1.4.1.12 2,4-DAPDH
-
 Fervidobacterium nodosum
1.4.1.26 2,4-DAPDH
-
 Fervidobacterium nodosum
1.4.1.26 2,4-diaminopentanoate dehydrogenase
-
 Fervidobacterium nodosum
1.4.1.26 Fnod_1646
-
 Fervidobacterium nodosum

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.4.1.12 85
-
-
 Fervidobacterium nodosum
1.4.1.26 85
-
-
 Fervidobacterium nodosum

Temperature Range [°C]

EC Number Temperature Minimum [°C] Temperature Maximum [°C] Comment Organism
1.4.1.26 70 100 more than 50% activity between 70 and 100°C Fervidobacterium nodosum

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.4.1.12 90
-
 the half-denaturation time at 90°C is 38 min and 2 min at 100°C Fervidobacterium nodosum
1.4.1.26 90 100 the half-denaturation time at 90°C and 100°C is 38 min and 2 min, respectively Fervidobacterium nodosum

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.4.1.12 0.0006
-
 (2R,5S)-2,5-diaminohexanoate at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 57
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 65
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 65
-
 (2R,4S)-2,4-diaminopentanoate at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 0.0006
-
 2,5-Diaminohexanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 57
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 65
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 65
-
 (2R,4S)-2,4-diaminopentanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.4.1.12 9.5
-
-
 Fervidobacterium nodosum
1.4.1.26 9.5
-
-
 Fervidobacterium nodosum

pH Range

EC Number pH Minimum pH Maximum Comment Organism
1.4.1.12 9 10 the enzyme shows more than 70% of maximum activity at pH 9.0-10.0 Fervidobacterium nodosum
1.4.1.26 9 10 the enzyme shows more than 70% of maximum activity in the pH range of 9.0-10.0 Fervidobacterium nodosum

Cofactor

EC Number Cofactor Comment Organism Structure
1.4.1.12 NAD+ the activity of the enzyme with NAD+ is 5.4times higher than that with NADP+ Fervidobacterium nodosum
1.4.1.12 NADP+ the activity of the enzyme with NAD+ is 5.4times higher than that with NADP+ Fervidobacterium nodosum
1.4.1.26 NAD+ the Km value for NAD+ is about 40 times lower than that for NADP+ Fervidobacterium nodosum
1.4.1.26 NADP+
-
 Fervidobacterium nodosum
1.4.1.26 pyridoxal 5'-phosphate
-
 Fervidobacterium nodosum

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
1.4.1.12 0.1
-
 D-ornithine at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 0.1
-
 D-ornithine at pH 8.5 and 55°C Fervidobacterium nodosum

General Information

EC Number General Information Comment Organism
1.4.1.12 metabolism the enzyme plays a regulatory role in the oxidative ornithine degradation pathway Fervidobacterium nodosum

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.4.1.12 29
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 330
-
 (2R,4S)-2,4-diaminopentanoate at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.12 1300
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 0.0003
-
 2,5-Diaminohexanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 29
-
 NADP+ at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 330
-
 (2R,4S)-2,4-diaminopentanoate with NAD+ as cosubstrate, at pH 8.5 and 55°C Fervidobacterium nodosum
1.4.1.26 1300
-
 NAD+ at pH 8.5 and 55°C Fervidobacterium nodosum