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Literature summary for 1.1.1.95 extracted from

  • Dey, S.; Burton, R.L.; Grant, G.A.; Sacchettini, J.C.
    Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase (2008), Biochemistry, 47, 8271-8282.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expression of tagged wild-type and mutant enzymes Mycobacterium tuberculosis

Crystallization (Commentary)

Crystallization (Comment) Organism
D-3-phosphoglycerate dehydrogenase with bound effector L-serine or with bound substrate hydroxypyruvic acid phosphate, PGDH at 10 mg/ml is mixed with 5 mM hydroxypyruvic acid phosphate and 5 mM NAD+ analogue 3-acetyl pyridine adenine dinucleotide, or with 5 mM NADH and 5 mM L-serine, from 1 M Na K tartrate, 0.1 M MES, pH 6.5, cryoprotection in 25% propylene glycol, X-ray diffraction structure determination and analysis at resolutions of 2.7 A and 2.4 A, respectively Mycobacterium tuberculosis

Protein Variants

Protein Variants Comment Organism
D463A site-directed mutagenesis, a very large reduction in the sensitivity of the mutant enzyme to L-serine Mycobacterium tuberculosis
G316V site-directed mutagenesis, the mutant shows slightly reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
G316V/G317V site-directed mutagenesis, the mutant shows reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
G316V/G317V/G318V site-directed mutagenesis, the mutant is not producable Mycobacterium tuberculosis
G316V/G318V site-directed mutagenesis, the mutant shows reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
G317V site-directed mutagenesis, the mutant shows slightly reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
G317V/G318V site-directed mutagenesis, the mutant shows reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
G318V site-directed mutagenesis, the mutant shows slightly reduced activity and decreased sensitivity to L-serine compared to the wild-type Mycobacterium tuberculosis
N481A site-directed mutagenesis, a very large reduction in the sensitivity of the mutant enzyme to L-serine. Mutant N481A co-elutes with native PGDH in gel filtration, it shows loss of cooperativity, which cannot be explained by a change in the quaternary structure of the enzyme from tetramer to dimer or monomer Mycobacterium tuberculosis
Y461A site-directed mutagenesis, a very large reduction in the sensitivity of the mutant enzyme to L-serine Mycobacterium tuberculosis

Inhibitors

Inhibitors Comment Organism Structure
L-serine
-
Mycobacterium tuberculosis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information stopped flow and steady-state kinetic analysis Mycobacterium tuberculosis
0.114
-
NADH pH 7.5, 25°C, recombinant mutant G316V Mycobacterium tuberculosis
0.12
-
NADH pH 7.5, 25°C, recombinant mutant N481A Mycobacterium tuberculosis
0.14
-
NADH pH 7.5, 25°C, recombinant mutant D463A Mycobacterium tuberculosis
0.165
-
NADH pH 7.5, 25°C, recombinant mutant G317V Mycobacterium tuberculosis
0.17
-
NADH pH 7.5, 25°C, wild-type enzyme Mycobacterium tuberculosis
0.203
-
NADH pH 7.5, 25°C, recombinant mutant G318V Mycobacterium tuberculosis
0.22
-
NADH pH 7.5, 25°C, recombinant mutant G317V/G318V Mycobacterium tuberculosis
0.27
-
NADH pH 7.5, 25°C, recombinant mutant Y461A Mycobacterium tuberculosis
0.47
-
NADH pH 7.5, 25°C, recombinant mutant G316V/G318V Mycobacterium tuberculosis
0.61
-
NADH pH 7.5, 25°C, recombinant mutant G316V/G317V Mycobacterium tuberculosis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
phosphonooxypyruvate + NADH + H+ Mycobacterium tuberculosis
-
?
-
?
phosphonooxypyruvate + NADH + H+ Mycobacterium tuberculosis H37Rv
-
?
-
?

Organism

Organism UniProt Comment Textmining
Mycobacterium tuberculosis P9WNX3
-
-
Mycobacterium tuberculosis H37Rv P9WNX3
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant tagged wild-type and mutant enzymes Mycobacterium tuberculosis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
phosphonooxypyruvate + NADH + H+
-
Mycobacterium tuberculosis ?
-
?
phosphonooxypyruvate + NADH + H+ very slow NADH binding in absence of substrate, productive NADH binding, that would support catalytic turnover, is dependent on the presence of substrate, active site structure with the catalytic His280, modelling of ligand-free and substrate-bound active site, overview Mycobacterium tuberculosis ?
-
?
phosphonooxypyruvate + NADH + H+
-
Mycobacterium tuberculosis H37Rv ?
-
?
phosphonooxypyruvate + NADH + H+ very slow NADH binding in absence of substrate, productive NADH binding, that would support catalytic turnover, is dependent on the presence of substrate, active site structure with the catalytic His280, modelling of ligand-free and substrate-bound active site, overview Mycobacterium tuberculosis H37Rv ?
-
?

Subunits

Subunits Comment Organism
More the apo-enzyme shows an extreme asymmetry in the orientation of the domains from one subunit to another. The poly glycine stretch in the loop that contains the locus for the 160° rotation leads to subunit asymmetry, structure modelling, overview Mycobacterium tuberculosis
tetramer ligand-bound enzyme, sequence comparison Mycobacterium tuberculosis

Synonyms

Synonyms Comment Organism
D-3-phosphoglycerate dehydrogenase
-
Mycobacterium tuberculosis
PGDH
-
Mycobacterium tuberculosis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Mycobacterium tuberculosis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
603
-
NADH pH 7.5, 25°C, recombinant mutant N481A Mycobacterium tuberculosis
605
-
NADH pH 7.5, 25°C, recombinant mutant G317V/G318V Mycobacterium tuberculosis
720
-
NADH pH 7.5, 25°C, recombinant mutant D463A Mycobacterium tuberculosis
1111
-
NADH pH 7.5, 25°C, recombinant mutant G316V Mycobacterium tuberculosis
2111
-
NADH pH 7.5, 25°C, recombinant mutant G317V Mycobacterium tuberculosis
2349
-
NADH pH 7.5, 25°C, recombinant mutant G318V Mycobacterium tuberculosis
2461
-
NADH pH 7.5, 25°C, wild-type enzyme Mycobacterium tuberculosis
2754
-
NADH pH 7.5, 25°C, recombinant mutant Y461A Mycobacterium tuberculosis
2805
-
NADH pH 7.5, 25°C, recombinant mutant G316V/G317V Mycobacterium tuberculosis
2827
-
NADH pH 7.5, 25°C, recombinant mutant G316V/G318V Mycobacterium tuberculosis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Mycobacterium tuberculosis

Cofactor

Cofactor Comment Organism Structure
NADH cofactor binding site structure and binding mechanism, overview Mycobacterium tuberculosis

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.22
-
L-serine pH 7.5, 25°C, recombinant mutant G316V/G318V Mycobacterium tuberculosis
0.38
-
L-serine pH 7.5, 25°C, recombinant mutant G316V/G317V Mycobacterium tuberculosis
0.42
-
L-serine pH 7.5, 25°C, recombinant mutant Y461A Mycobacterium tuberculosis
0.95
-
L-serine pH 7.5, 25°C, wild-type enzyme Mycobacterium tuberculosis
1.09
-
L-serine pH 7.5, 25°C, recombinant mutant D463A Mycobacterium tuberculosis
1.11
-
L-serine pH 7.5, 25°C, recombinant mutant G317V Mycobacterium tuberculosis
1.62
-
L-serine pH 7.5, 25°C, recombinant mutant G317V/G318V Mycobacterium tuberculosis
1.925
-
L-serine pH 7.5, 25°C, recombinant mutant G318V Mycobacterium tuberculosis
2.231
-
L-serine pH 7.5, 25°C, recombinant mutant G316V Mycobacterium tuberculosis
2.32
-
L-serine pH 7.5, 25°C, recombinant mutant N481A Mycobacterium tuberculosis