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Literature summary for 3.5.1.19 extracted from

  • Smith, B.C.; Anderson, M.A.; Hoadley, K.A.; Keck, J.L.; Cleland, W.W.; Denu, J.M.
    Structural and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces cerevisiae (2012), Biochemistry, 51, 243-256.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Saccharomyces cerevisiae

Crystallization (Commentary)

Crystallization (Comment) Organism
in complex with nicotinaldehyde, hanging drop vapor diffusion method, using 1.6 M NaOAc, 10% (w/v) ethylene glycol, and 0.1 M HEPES (pH 7.4) Saccharomyces cerevisiae

Protein Variants

Protein Variants Comment Organism
C167A the mutant shows most strongly decreased kcat value compared to the wild type enzyme (below the assay detection limit) Saccharomyces cerevisiae
D51A the zinc-binding mutant shows decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
D51N the zinc-binding mutant shows decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
D8A the mutant shows 770fold decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
D8E the mutant shows 100fold decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
D8N the mutant shows 1000fold decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
H53A the zinc-binding mutant shows decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
H94A the zinc-binding mutant shows decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
K122A the mutant shows 16fold decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae
K122R the mutant shows 770fold decreased kcat value compared to the wild type enzyme Saccharomyces cerevisiae

Inhibitors

Inhibitors Comment Organism Structure
3-acetylpyridine competitive inhibition Saccharomyces cerevisiae
benzaldehyde competitive inhibition Saccharomyces cerevisiae
additional information not inhibited by 10 mM EDTA Saccharomyces cerevisiae
nicotinaldehyde most potent inhibitor Saccharomyces cerevisiae
nicotinic acid competitive inhibition Saccharomyces cerevisiae
pyrazinoic acid competitive inhibition Saccharomyces cerevisiae

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0018
-
nicotinamide Km below 0.0018 mM, mutant enzyme D51N, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0024
-
nicotinamide Km below 0.0024 mM, mutant enzyme D51A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0027
-
nicotinamide Km below 0.0027 mM, mutant enzyme H94A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0065
-
nicotinamide Km below 0.0065 mM, mutant enzyme K122A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0065
-
nicotinamide mutant enzyme H53A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0096
-
nicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.025
-
Benzamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.061
-
5-Methylnicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.157
-
Pyrazinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae

Metals/Ions

Metals/Ions Comment Organism Structure
Zn2+ contains tightly bound zinc. Addition of 2 mM ZnCl2 fails to increase the activity of the wild type enzyme Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
nicotinamide + H2O Saccharomyces cerevisiae best substrate nicotinate + NH3
-
?

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae P53184
-
-

Purification (Commentary)

Purification (Comment) Organism
Ni-NTA column chromatography and Sephacryl S-300 gel filtration Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1-methylnicotinamide + H2O
-
Saccharomyces cerevisiae 1-methylnicotinate + NH3
-
?
5-methylnicotinamide + H2O
-
Saccharomyces cerevisiae 5-methylnicotinate + NH3
-
?
benzamide + H2O
-
Saccharomyces cerevisiae benzoate + NH3
-
?
additional information no activity with nicotinamide mononucleotide and NAD+ Saccharomyces cerevisiae ?
-
?
nicotinamide + H2O best substrate Saccharomyces cerevisiae nicotinate + NH3
-
?
pyrazinamide + H2O
-
Saccharomyces cerevisiae pyrazine-2-carboxylic acid + NH3
-
?
thionicotinamide + H2O
-
Saccharomyces cerevisiae pyridine-3-carbothioic O-acid
-
?

Synonyms

Synonyms Comment Organism
Pnc1
-
Saccharomyces cerevisiae

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0005
-
nicotinamide kcat below 0.0005 s-1, mutant enzyme C167A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0006
-
nicotinamide mutant enzyme D8E, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0009
-
nicotinamide mutant enzyme D8A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0009
-
nicotinamide mutant enzyme D8N, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0009
-
nicotinamide mutant enzyme K122R, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.007
-
nicotinamide mutant enzyme D51A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0088
-
Benzamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.014
-
nicotinamide mutant enzyme H53A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.02
-
nicotinamide mutant enzyme H94A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.044
-
nicotinamide mutant enzyme K122A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.064
-
nicotinamide mutant enzyme D51N, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.69
-
nicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
1.75
-
5-Methylnicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
2.56
-
Pyrazinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7 8
-
Saccharomyces cerevisiae

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.00094
-
nicotinaldehyde wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0206
-
benzaldehyde wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.12
-
nicotinic acid wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.316
-
3-acetylpyridine wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
6.7
-
pyrazinoic acid wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.0086
-
1-methylnicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.0096
-
nicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.025
-
Benzamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.05
-
Thionicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.061
-
5-Methylnicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.157
-
Pyrazinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
0.35
-
Benzamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
2.2
-
nicotinamide mutant enzyme H53A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
6.7
-
nicotinamide kcat/Km above 6.7 (1/sec*mM), mutant enzyme K122A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
7.4
-
nicotinamide kcat/Km above 7.4 (1/sec*mM), mutant enzyme H94A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
8.3
-
nicotinamide kcat/Km above 8.3 (1/sec*mM), mutant enzyme D51A, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
16
-
Pyrazinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
29
-
5-Methylnicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
35
-
nicotinamide kcat/Km above 35 (1/sec*mM), mutant enzyme D51N, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae
72
-
nicotinamide wild type enzyme, in 50 mM sodium phosphate (pH 7.5), at 25°C Saccharomyces cerevisiae