Literature summary for 1.1.1.87 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 .

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Protein Variants	Comment	Organism
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
L81P	the mutant shows decreased catalytic efficiency with homoisocitrate, isocitrate and 3-isopropylmalate compared to the wild type enzyme	Thermococcus kodakarensis
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
S80A	the mutant shows decreased catalytic efficiency with homoisocitrate, isocitrate and 3-isopropylmalate compared to the wild type enzyme	Thermococcus kodakarensis
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]

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

Metals/Ions

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

Molecular Weight [Da]

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

Organism

Organism	UniProt	Comment	Textmining
Thermococcus kodakarensis	-	-	-
Thermococcus kodakarensis KUW1	-	-	-

Purification (Commentary)

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
homotetramer	x-ray crystallography	Thermococcus kodakarensis

Synonyms

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

Turnover Number [1/s]

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

Cofactor

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

General Information

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

kcat/KM [mM/s]

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