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Literature summary for 1.1.1.387 extracted from

  • Tchigvintsev, A.; Singer, A.; Brown, G.; Flick, R.; Evdokimova, E.; Tan, K.; Gonzalez, C.F.; Savchenko, A.; Yakunin, A.F.
    Biochemical and structural studies of uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed NAD+-dependent L-serine dehydrogenase (2012), J. Biol. Chem., 287, 1874-1883.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
overexpressed in Escherichia coli Pseudomonas aeruginosa

Crystallization (Commentary)

Crystallization (Comment) Organism
two crystal structures of the enzyme are solved at 2.2-2.3 A resolution and reveal an N-terminal Rossmann fold domain connected by a long alpha-helix to the C-terminal all-alpha-domain. The apostructure shows the presence of additional density modeled as HEPES bound in the interdomain cleft close to the predicted catalytic Lys171, revealing the molecular details of the enzyme substrate-binding site. The structure of the enzyme-NAD complex demonstrates that the opposite side of the enzyme active site accommodates the cofactor, which is also bound near Lys171. Crystals of the enzyme are grown at 21C by the hanging drop vapor diffusion method with 0.002 ml of protein sample mixed with an equal volume of the reservoir buffer. The crystals of the wild-type enzyme grew after 1 week in the presence of 4 M ammonium acetate and 0.1 M sodium acetate (pH 5.4). The crystals of the complex of the enzyme with NAD+ are obtained by soaking the crystals in 10 mM NAD+. For diffraction studies, the crystals are stabilized with the crystallization buffer supplemented with 12% ethylene glycol as a cryoprotectant and flash frozen in liquid nitrogen Pseudomonas aeruginosa

Protein Variants

Protein Variants Comment Organism
D247A inactive protein Pseudomonas aeruginosa
K171A inactive protein Pseudomonas aeruginosa
K246A inactive protein Pseudomonas aeruginosa
N175A mutant enzyme with very low activity Pseudomonas aeruginosa
S122A mutant enzyme with very low activity Pseudomonas aeruginosa
T96A mutant enzyme with very low activity Pseudomonas aeruginosa
W214A inactive protein Pseudomonas aeruginosa
Y219A mutant enzyme with very low activity Pseudomonas aeruginosa

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.4
-
DL-threonine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
2.5
-
L-serine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
3.4
-
NAD+ pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
4.2
-
L-serine pH 11.0, 37°C, mutant enzyme N175A Pseudomonas aeruginosa
10.6
-
L-serine pH 11.0, 37°C, mutant enzyme S122A Pseudomonas aeruginosa
10.8
-
D-glycerate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
11
-
L-serine pH 11.0, 37°C, mutant enzyme Y219A Pseudomonas aeruginosa
12.3
-
L-serine pH 11.0, 37°C, mutant enzyme T96A Pseudomonas aeruginosa
17.4
-
methyl 2,2-dimethyl-3-hydroxypropionate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
L-serine + NAD+ Pseudomonas aeruginosa the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases ?
-
?

Organism

Organism UniProt Comment Textmining
Pseudomonas aeruginosa Q9I5I6
-
-

Purification (Commentary)

Purification (Comment) Organism
-
Pseudomonas aeruginosa

Reaction

Reaction Comment Organism Reaction ID
2-aminomalonate semialdehyde = 2-aminoacetaldehyde + CO2 (1b), spontaneous Pseudomonas aeruginosa
L-serine + NAD+ = 2-aminoacetaldehyde + CO2 + NADH + H+ overall reaction Pseudomonas aeruginosa
L-serine + NAD+ = 2-aminomalonate semialdehyde + NADH + H+ (1a) Pseudomonas aeruginosa

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
D-glycerate + NAD+
-
Pseudomonas aeruginosa ?
-
?
DL-threonine + NAD+
-
Pseudomonas aeruginosa ?
-
?
L-serine + NAD+ the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases Pseudomonas aeruginosa ?
-
?
L-serine + NAD+ the enzyme might be involved in serine/methylserine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases Pseudomonas aeruginosa ?
-
?
methyl 2,2-dimethyl-3-hydroxypropionate + NAD+
-
Pseudomonas aeruginosa ?
-
?

Synonyms

Synonyms Comment Organism
NAD+-dependent L-serine dehydrogenase
-
Pseudomonas aeruginosa
PA0743
-
Pseudomonas aeruginosa

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Pseudomonas aeruginosa

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.4
-
L-serine pH 11.0, 37°C, mutant enzyme S122A Pseudomonas aeruginosa
0.8
-
L-serine pH 11.0, 37°C, mutant enzyme Y219A Pseudomonas aeruginosa
1.4
-
L-serine pH 11.0, 37°C, mutant enzyme T96A Pseudomonas aeruginosa
1.6
-
NAD+ pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
2.7
-
L-serine pH 11.0, 37°C, mutant enzyme N175A Pseudomonas aeruginosa
5.8
-
D-glycerate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
9.6
-
DL-threonine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
10.4
-
L-serine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
11.6
-
methyl 2,2-dimethyl-3-hydroxypropionate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
10 11
-
Pseudomonas aeruginosa

Cofactor

Cofactor Comment Organism Structure
NAD+ the enzyme can also use NADP+ as a cofactor for the oxidation of L-serine, but this activity is significantly lower than that with NAD+ (4–6%) Pseudomonas aeruginosa
NADP+ the enzyme can also use NADP+ as a cofactor for the oxidation of L-serine, but this activity is significantly lower than that with NAD+ (4–6%) Pseudomonas aeruginosa

General Information

General Information Comment Organism
metabolism the enzyme might be involved in serine/threonine degradation. Since growth experiments with various nitrogen and carbon sources (including L-serine) reveal no difference between the Pseudomonas aeruginosa wild-type and PA0743 deletion strains, it is suggested hat this organism might contain other (complementing) serine dehydrogenases Pseudomonas aeruginosa

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.04
-
L-serine pH 11.0, 37°C, mutant enzyme S122A Pseudomonas aeruginosa
0.07
-
L-serine pH 11.0, 37°C, mutant enzyme Y219A Pseudomonas aeruginosa
0.1
-
L-serine pH 11.0, 37°C, mutant enzyme T96A Pseudomonas aeruginosa
0.3
-
D-glycerate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
0.5
-
NAD+ pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
0.6
-
L-serine pH 11.0, 37°C, mutant enzyme N175A Pseudomonas aeruginosa
0.7
-
methyl 2,2-dimethyl-3-hydroxypropionate pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
4
-
L-serine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa
4
-
DL-threonine pH 11.0, 37°C, wild-type enzyme Pseudomonas aeruginosa