Literature summary for 4.1.1.25 extracted from

Zhu, H.; Xu, G.; Zhang, K.; Kong, X.; Han, R.; Zhou, J.; Ni, Y.
Crystal structure of tyrosine decarboxylase and identification of key residues involved in conformational swing and substrate binding (2016), Sci. Rep., 6, 27779 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene tdc, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)	Levilactobacillus brevis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified His-tagged enzyme as apoenzyme and in complex with pyridoxal 5'-phosphate (PLP), sitting drop vapor diffusion method, mixing of 0.002 ml of 10 mg/ml protein solution with 0.002 ml of reservoir solution containing 0.1 M sodium cacodylate trihydrate, pH 7.5, 0.2 M MgCl2, and 18% PEG 1000, for the SeMet-LbTDC enzyme variant 0.1 M sodium cacodylate trihydrate, pH 7.0, 0.1 M MgCl2, and 16% PEG 4000 is used, the LbTDC-PLP complex is also crystallized at a molar ratio of 1:4 under the same conditions as SeMet-LbTDC, 2-5 days, 18°C, X-ray diffraction structure determination and analysis at 1.73-1.90 A resolution	Levilactobacillus brevis

Crystallization (Comment)

Organism

purified His-tagged enzyme as apoenzyme and in complex with pyridoxal 5'-phosphate (PLP), sitting drop vapor diffusion method, mixing of 0.002 ml of 10 mg/ml protein solution with 0.002 ml of reservoir solution containing 0.1 M sodium cacodylate trihydrate, pH 7.5, 0.2 M MgCl2, and 18% PEG 1000, for the SeMet-LbTDC enzyme variant 0.1 M sodium cacodylate trihydrate, pH 7.0, 0.1 M MgCl2, and 16% PEG 4000 is used, the LbTDC-PLP complex is also crystallized at a molar ratio of 1:4 under the same conditions as SeMet-LbTDC, 2-5 days, 18°C, X-ray diffraction structure determination and analysis at 1.73-1.90 A resolution

Levilactobacillus brevis

Protein Variants

Protein Variants	Comment	Organism
A295F	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
E102A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
E299A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
G296F	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
H241N	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
H241Q	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
H391A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
H98A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
K240A	site-directed saturation mutagenesis, the mutant shows 36% reduced catalytic efficiency compared to wild-type	Levilactobacillus brevis
M505A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
M588A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
M99A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
additional information	structure-guided site-directed mutagenesis and alanine scanning and saturation mutagenesis of LbTDC are performed on residues around the substrate binding sites and those required for conformational stability to elucidate the function of key residues involved in the catalytic mechanism and to promote the potential applications of LbTDC in tyramine synthesis, food safety, and pharmacology	Levilactobacillus brevis
N100A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
P397A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
S101A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
S297A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
S586A	site-directed saturation mutagenesis, the mutant variant displays 278% of the catalytic efficiency of the wild-type and increased substrate affinity, which is attributed to decreased steric hindrance and increased hydrophobicity	Levilactobacillus brevis
S586C	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586D	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586E	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
S586F	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
S586G	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
S586H	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586I	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
S586K	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586L	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
S586M	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586N	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586P	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586Q	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586R	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586T	site-directed saturation mutagenesis, the mutant highly shows reduced activity compared to wild-type	Levilactobacillus brevis
S586V	site-directed saturation mutagenesis, the mutant highly shows reduced activity compared to wild-type	Levilactobacillus brevis
S586W	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
S586Y	site-directed saturation mutagenesis, inactive mutant	Levilactobacillus brevis
T103A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
T298A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
V294A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
V396A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
Y331A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
Y395A	site-directed saturation mutagenesis, the mutant shows reduced activity compared to wild-type	Levilactobacillus brevis
Y398A	site-directed saturation mutagenesis, almost inactive mutant	Levilactobacillus brevis
Y398F	site-directed saturation mutagenesis, the mutant shows highly reduced activity compared to wild-type	Levilactobacillus brevis
Y420A	site-directed mutagenesis, inactive mutant	Levilactobacillus brevis
Y420F	site-directed mutagenesis, inactive mutant	Levilactobacillus brevis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.4	-	L-tyrosine	purified recombinant mutant S586A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.6	-	L-tyrosine	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.7	-	L-Dopa	purified recombinant mutants S586A and Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.8	-	L-Dopa	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
1.1	-	L-Dopa	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
1.6	-	L-tyrosine	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
1.7	-	L-Dopa	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
2.4	-	L-tyrosine	purified recombinant mutant Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
3	-	L-tyrosine	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
L-Tyrosine	Levilactobacillus brevis	-	Tyramine + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Levilactobacillus brevis	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, desalting gel filtration, and ultrafiltration	Levilactobacillus brevis

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
0.2	-	purified recombinant mutant H241N, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.3	-	purified recombinant mutant H241Q, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.6	-	purified recombinant mutant Y398A, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
0.8	-	purified recombinant mutant Y398A, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
1.9	-	purified recombinant mutant H241Q, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
3.2	-	purified recombinant mutant Y398F, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
4.2	-	purified recombinant mutant Y398F, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
20.1	-	purified recombinant mutant K240A, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
26.5	-	purified recombinant His-tagged wild-type enzyme, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
43.1	-	purified recombinant His-tagged wild-type enzyme, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
43.7	-	purified recombinant mutant S586A, substrate L-dopa, pH 5.0-7.4, 40°C	Levilactobacillus brevis
56.8	-	purified recombinant mutant K240A, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis
96	-	purified recombinant mutant S586A, substrate L-tyrosine, pH 5.0-7.4, 40°C	Levilactobacillus brevis

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
L-Dopa	shows about half of the catalytic efficiency compared to L-tyrosine	Levilactobacillus brevis	dopamine + CO2	-	?
L-Tyrosine	-	Levilactobacillus brevis	Tyramine + CO2	-	?
L-Tyrosine	preferred substrate	Levilactobacillus brevis	Tyramine + CO2	-	?
additional information	key residues involved in conformational swing and substrate binding, e.g. H241, K240, or S586, molecular docking and mutational analysis, overview. Residue S586 is a critical residue for substrate binding	Levilactobacillus brevis	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	enzyme LbTDC is a homodimer, and the two subunits exist in an asymmetric form, structure comparisons, overview	Levilactobacillus brevis

Synonyms

Synonyms	Comment	Organism
LbTDC	-	Levilactobacillus brevis
TDC	-	Levilactobacillus brevis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
40	-	assay at	Levilactobacillus brevis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
2.5	-	L-Dopa	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
9.8	-	L-tyrosine	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
12.3	-	L-Dopa	purified recombinant mutant Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
31.9	-	L-tyrosine	purified recombinant mutant Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
64.7	-	L-Dopa	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
76.5	-	L-Dopa	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
124.8	-	L-tyrosine	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
126	-	L-Dopa	purified recombinant mutant S586A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
224.5	-	L-tyrosine	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
250.9	-	L-tyrosine	purified recombinant mutant S586A, pH 5.0-7.4, 40°C	Levilactobacillus brevis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
5	7.4	assay at	Levilactobacillus brevis

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	PLP, dependent on	Levilactobacillus brevis

General Information

General Information	Comment	Organism
evolution	tyrosine decarboxylase (TyDC) is a type II pyridoxal 5'-phosphate decarboxylase and shares high identity with 3,4-dihydroxy-L-phenylalanine (DOPA) decarboxylase (DDC), glutamic acid decarboxylase (GAD), and histidine decarboxylase (HDC). From an evolutionary point of view, the TDC system in Lactobacillus brevis is responsible for tyramine formation in response to acid challenge. The TDC system can generate a proton motive force (PMF) through proton consumption in the decarboxylation reaction and the membrane potential resulting from electrogenic transport of tyrosine in exchange for its corresponding biogenic amine tyramine	Levilactobacillus brevis
physiological function	the TDC system can generate a proton motive force (PMF) through proton consumption in the decarboxylation reaction and the membrane potential resulting from electrogenic transport of tyrosine in exchange for its corresponding biogenic amine tyramine	Levilactobacillus brevis

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
1.5	-	L-Dopa	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
3.4	-	L-tyrosine	purified recombinant mutant Y398A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
13.5	-	L-tyrosine	purified recombinant mutant Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
18.4	-	L-Dopa	purified recombinant mutant Y398F, pH 5.0-7.4, 40°C	Levilactobacillus brevis
58.3	-	L-Dopa	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
101.1	-	L-Dopa	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
139.4	-	L-tyrosine	purified recombinant mutant K240A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
181.3	-	L-Dopa	purified recombinant mutant S586A, pH 5.0-7.4, 40°C	Levilactobacillus brevis
216	-	L-tyrosine	purified recombinant His-tagged wild-type enzyme, pH 5.0-7.4, 40°C	Levilactobacillus brevis
600.4	-	L-tyrosine	purified recombinant mutant S586A, pH 5.0-7.4, 40°C	Levilactobacillus brevis