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Literature summary extracted from

  • Shimizu, T.; Yin, L.; Yoshida, A.; Yokooji, Y.; Hachisuka, S.; Sato, T.; Tomita, T.; Nishida, H.; Atomi, H.; Kuzuyama, T.; Nishiyama, M.
    Structure and function of an ancestral-type beta-decarboxylating dehydrogenase from Thermococcus kodakarensis (2017), Biochem. J., 474, 105-122 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.87 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL cells Thermococcus kodakarensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.87 His6-tagged recombinant apoenzyme, hanging drop vapor diffusion method, using 100 mM HEPES-NaOH (pH 7.5), 200 mM NaCl, and 10% (v/v) 2-propanol. Enzyme in complex with homoisocitrate and Mn2+, hanging drop vapor diffusion method, using 100 mM HEPES-NaOH (pH 7.5), 200 mM NaCl, and 10% (v/v) 2-propanol. Enzyme in complex with isocitrate and Mn2+, hanging drop vapor diffusion method, using 100 mM Tris-HCl (pH 7.5), 200 mM NaCl, and 30% (v/v) 2-methyl-2,4-pentanediol. Enzyme in complex with 3-isopropylmalate and Mn2+, hanging drop vapor diffusion method, using 100 mM HEPES-NaOH (pH 7.5), 200 mM NaCl, and 36% (v/v) 2-methyl-2,4-pentanediol Thermococcus kodakarensis

Protein Variants

EC Number Protein Variants Comment Organism
1.1.1.87 I82N the mutant shows decreased catalytic efficiency with homoisocitrate and isocitrate compared to the wild type enzyme and has no activity with 3-isopropylmalate Thermococcus kodakarensis
1.1.1.87 L81P the mutant shows decreased catalytic efficiency with homoisocitrate, isocitrate and 3-isopropylmalate compared to the wild type enzyme Thermococcus kodakarensis
1.1.1.87 L83R the mutant shows decreased catalytic efficiency with homoisocitrate and isocitrate compared to the wild type enzyme and has no activity with 3-isopropylmalate Thermococcus kodakarensis
1.1.1.87 S80A the mutant shows decreased catalytic efficiency with homoisocitrate, isocitrate and 3-isopropylmalate compared to the wild type enzyme Thermococcus kodakarensis
1.1.1.87 T71V the mutant shows decreased catalytic efficiency with homoisocitrate and isocitrate, as well as increased catalytic efficiency with 3-isopropylmalate compared to the wild type enzyme Thermococcus kodakarensis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.87 0.0073
-
 homoisocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.014
-
 isocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.036
-
 NAD+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.037
-
 homoisocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.042
-
 homoisocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.05
-
 3-isopropylmalate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.064
-
 homoisocitrate wild type enzyme, with NADP+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.1
-
 NAD+ wild type enzyme, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.16
-
 NAD+ mutant enzyme L83R, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.17
-
 homoisocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.25
-
 NAD+ mutant enzyme T71V, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.3
-
 isocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.31
-
 3-isopropylmalate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.32
-
 NAD+ mutant enzyme L81P, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.46
-
 homoisocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.5
-
 isocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.58
-
 isocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.6
-
 NAD+ mutant enzyme L81P, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.62
-
 NAD+ mutant enzyme L83R, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.64
-
 NAD+ mutant enzyme I82N, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.68
-
 3-isopropylmalate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.71
-
 3-isopropylmalate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.76
-
 NAD+ mutant enzyme S80A, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.92
-
 NAD+ mutant enzyme S80A, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.92
-
 NAD+ wild type enzyme, with D-malate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.94
-
 homoisocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1
-
 NAD+ mutant enzyme T71V, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.2
-
 isocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.2
-
 NAD+ mutant enzyme S80A, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.3
-
 NAD+ mutant enzyme L81P, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.5
-
 NAD+ mutant enzyme T71V, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.5
-
 NAD+ wild type enzyme, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.8
-
 NAD+ mutant enzyme I82N, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 2.2
-
 isocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 4.5
-
 D-malate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 7.6
-
 NADP+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.87 Mg2+ Mn2+ or Mg2+ is required for this activity, and stronger activity is observed with Mn2+ Thermococcus kodakarensis
1.1.1.87 Mn2+ Mn2+ or Mg2+ is required for this activity, and stronger activity is observed with Mn2+ Thermococcus kodakarensis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.1.1.87 238300
-
 gel filtration Thermococcus kodakarensis

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.87 Thermococcus kodakarensis
-
-
-
1.1.1.87 Thermococcus kodakarensis KUW1
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.87 Ni-NTA His-Bind column chromatography Thermococcus kodakarensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.87 3-isopropylmalate + NAD+ the enzyme has low catalytic efficiency toward 3-isopropylmalate Thermococcus kodakarensis alpha-ketoisocaproate + NADH + H+ + CO2
-
 ?
1.1.1.87 3-isopropylmalate + NAD+ the enzyme has low catalytic efficiency toward 3-isopropylmalate Thermococcus kodakarensis KUW1 alpha-ketoisocaproate + NADH + H+ + CO2
-
 ?
1.1.1.87 D-malate + NAD+ weak activity Thermococcus kodakarensis ?
-
 ?
1.1.1.87 D-malate + NAD+ weak activity Thermococcus kodakarensis KUW1 ?
-
 ?
1.1.1.87 homoisocitrate + NAD+ highest activity Thermococcus kodakarensis alpha-ketoadipate + NADH + H+ + CO2
-
 r
1.1.1.87 homoisocitrate + NAD+ highest activity Thermococcus kodakarensis KUW1 alpha-ketoadipate + NADH + H+ + CO2
-
 r
1.1.1.87 homoisocitrate + NADP+
-
 Thermococcus kodakarensis alpha-ketoadipate + NADPH + H+ + CO2
-
 r
1.1.1.87 isocitrate + NADP+
-
 Thermococcus kodakarensis 2-oxoglutarate + NADPH + H+ + CO2
-
 ?
1.1.1.87 isocitrate + NADP+
-
 Thermococcus kodakarensis KUW1 2-oxoglutarate + NADPH + H+ + CO2
-
 ?
1.1.1.87 additional information no activity with L-tartrate Thermococcus kodakarensis ?
-
-
1.1.1.87 additional information no activity with L-tartrate Thermococcus kodakarensis KUW1 ?
-
-

Subunits

EC Number Subunits Comment Organism
1.1.1.87 homotetramer x-ray crystallography Thermococcus kodakarensis

Synonyms

EC Number Synonyms Comment Organism
1.1.1.87 beta-decarboxylating dehydrogenase
-
 Thermococcus kodakarensis
1.1.1.87 HIc dehydrogenase
-
 Thermococcus kodakarensis
1.1.1.87 HICDH
-
 Thermococcus kodakarensis
1.1.1.87 TK0280
-
 Thermococcus kodakarensis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.87 0.099
-
 NAD+ wild type enzyme, with D-malate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.099
-
 D-malate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.22
-
 isocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.71
-
 isocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1
-
 isocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.1
-
 isocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.5
-
 3-isopropylmalate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 2.3
-
 3-isopropylmalate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 4.8
-
 homoisocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 4.8
-
 NAD+ wild type enzyme, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 4.8
-
 3-isopropylmalate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 5
-
 NAD+ wild type enzyme, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 5
-
 isocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 6.6
-
 isocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 6.9
-
 homoisocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 9.4
-
 3-isopropylmalate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 12
-
 NADP+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 12
-
 homoisocitrate wild type enzyme, with NADP+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 13
-
 homoisocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 17
-
 NAD+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 17
-
 homoisocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 43
-
 homoisocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 45
-
 homoisocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.87 NAD+ the enzyme prefers NAD+ to NADP+ as the coenzyme Thermococcus kodakarensis
1.1.1.87 NADP+
-
 Thermococcus kodakarensis

General Information

EC Number General Information Comment Organism
1.1.1.87 metabolism the enzyme is involved in lysine biosynthesis Thermococcus kodakarensis

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.87 0.022
-
 D-malate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.11
-
 NAD+ wild type enzyme, with D-malate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.44
-
 isocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.45
-
 isocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.56
-
 NAD+ mutant enzyme I82N, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.88
-
 NAD+ mutant enzyme T71V, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.92
-
 isocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 0.93
-
 NAD+ mutant enzyme S80A, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.2
-
 NAD+ mutant enzyme L81P, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.6
-
 NADP+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.8
-
 NAD+ mutant enzyme L81P, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 1.9
-
 NAD+ mutant enzyme S80A, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 2.2
-
 3-isopropylmalate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 2.4
-
 isocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 3.2
-
 NAD+ mutant enzyme T71V, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 3.2
-
 NAD+ wild type enzyme, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 5.1
-
 homoisocitrate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 7.5
-
 NAD+ mutant enzyme S80A, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 9.4
-
 NAD+ mutant enzyme T71V, with 3-isopropylmalate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 11
-
 NAD+ mutant enzyme L83R, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 11
-
 isocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 13
-
 3-isopropylmalate mutant enzyme T71V, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 15
-
 3-isopropylmalate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 41
-
 NAD+ mutant enzyme L81P, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 46
-
 3-isopropylmalate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 50
-
 NAD+ wild type enzyme, with isocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 70
-
 NAD+ mutant enzyme I82N, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 98
-
 homoisocitrate mutant enzyme I82N, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 190
-
 homoisocitrate mutant enzyme S80A, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 190
-
 homoisocitrate wild type enzyme, with NADP+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 250
-
 homoisocitrate mutant enzyme L83R, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 270
-
 NAD+ mutant enzyme L83R, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 310
-
 homoisocitrate mutant enzyme L81P, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 360
-
 isocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 470
-
 NAD+ wild type enzyme, with homoisocitrate as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis
1.1.1.87 2300
-
 homoisocitrate wild type enzyme, with NAD+ as cosubstrate, at pH 8.0 and 60°C Thermococcus kodakarensis