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Literature summary for 4.1.3.17 extracted from

  • Mazurkewich, S.; Wang, W.; Seah, S.Y.
    Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases (2014), Biochemistry, 53, 542-553.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
phylogenetic analysis Pseudomonas putida

Protein Variants

Protein Variants Comment Organism
E199A site-directed mutagenesis, the mutant shows reduced activity and reduced affinity for Co2+ compared to the wild-type enzyme Pseudomonas putida

Inhibitors

Inhibitors Comment Organism Structure
oxalate competitive inhibition Pseudomonas putida
oxalate competitive inhibition Saccharomyces cerevisiae
oxalate competitive inhibition Thermus thermophilus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.1265
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
0.1507
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
0.1876
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida
0.7086
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida

Metals/Ions

Metals/Ions Comment Organism Structure
Co2+ required, best activating metal ion, Km is 0.00838 mM for the wild-type enzyme, and 0.446 mM for the mutant E199A Pseudomonas putida
Co2+ required, equally activating as Ni2+ Thermus thermophilus
Mg2+ a magnesium ion is coordinated directly or indirectly via water through interactions with Asp102, Asp124, and Glu199 Pseudomonas putida
additional information the enzyme is a class II divalent metal ion-dependent aldolase Thermus thermophilus
additional information the enzyme is a class II divalent metal ion-dependent aldolase Saccharomyces cerevisiae
additional information the enzyme is a class II divalent metal ion-dependent aldolase. Coordination of a metal ion to support the binding of a pyruvyl moiety in the class II aldolase is essential, metal binding Glu199 residue Pseudomonas putida
Ni2+ required, best activating metal ion Saccharomyces cerevisiae
Ni2+ required, equally activating as Co2+ Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4-hydroxy-4-methyl-2-oxoglutarate Pseudomonas putida
-
2 pyruvate
-
?
additional information Pseudomonas putida the enzyme is a class II, divalent metal ion-dependent, pyruvate aldolase that catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate and 4-carboxy-4-hydroxy-2-oxoadipate into two molecules of pyruvate in the former and a molecule of each pyruvate and oxaloacetate in the latter, cf. 4-carboxy-4-hydroxy-2-oxoadipate aldolase, EC 4.1.3. The enzyme also contains a secondary oxaloacetate decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retroaldol and decarboxylase reactions ?
-
?

Organism

Organism UniProt Comment Textmining
Pseudomonas putida
-
-
-
Saccharomyces cerevisiae
-
-
-
Thermus thermophilus
-
-
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4-hydroxy-4-methyl-2-oxoglutarate
-
Thermus thermophilus 2 pyruvate
-
?
4-hydroxy-4-methyl-2-oxoglutarate
-
Saccharomyces cerevisiae 2 pyruvate
-
?
4-hydroxy-4-methyl-2-oxoglutarate
-
Pseudomonas putida 2 pyruvate
-
?
4-hydroxy-4-methyl-2-oxoglutarate
-
Thermus thermophilus HB8 / ATCC 27634 / DSM 579 2 pyruvate
-
?
additional information the enzyme is a class II, divalent metal ion-dependent, pyruvate aldolase that catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate and 4-carboxy-4-hydroxy-2-oxoadipate into two molecules of pyruvate in the former and a molecule of each pyruvate and oxaloacetate in the latter, cf. 4-carboxy-4-hydroxy-2-oxoadipate aldolase, EC 4.1.3. The enzyme also contains a secondary oxaloacetate decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retroaldol and decarboxylase reactions Pseudomonas putida ?
-
?
additional information the RNAse E activity A-like protein TtRraA from Thermus thermophilus HB8 contains HMG aldolase and oxaloacetate decarboxylase activities Thermus thermophilus ?
-
?
additional information the RNAse E activity A-like protein Yer010Cp from Saccharomyces cerevisiae S288C contains HMG aldolase and oxaloacetate decarboxylase activities Saccharomyces cerevisiae ?
-
?
additional information the RNAse E activity A-like protein TtRraA from Thermus thermophilus HB8 contains HMG aldolase and oxaloacetate decarboxylase activities Thermus thermophilus HB8 / ATCC 27634 / DSM 579 ?
-
?

Subunits

Subunits Comment Organism
trimer
-
Pseudomonas putida

Synonyms

Synonyms Comment Organism
4-hydroxy-4-methyl-2-oxoglutarate aldolase
-
Pseudomonas putida
4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase
-
Pseudomonas putida
HMG aldolase
-
Thermus thermophilus
HMG aldolase
-
Saccharomyces cerevisiae
HMG aldolase
-
Pseudomonas putida
HMG/CHA aldolase
-
Pseudomonas putida

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Thermus thermophilus
25
-
assay at Saccharomyces cerevisiae
25
-
assay at Pseudomonas putida

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0276
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
0.061
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida
0.356
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
15.6
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Thermus thermophilus
8
-
assay at Saccharomyces cerevisiae
8
-
assay at Pseudomonas putida

Ki Value [mM]

Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
0.0319
-
oxalate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
0.0377
-
oxalate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus

General Information

General Information Comment Organism
evolution RNase E activity A, RraA, like protein (RraA-like protein) TtRraA from Thermus thermophilus HB8 (TtRraA) contains HMG aldolase and oxaloacetate decarboxylase activities. The enzyme TtRraA contains a G-X20-R-D-X2-E/D motif Thermus thermophilus
evolution RNase E activity A, RraA, like proteins TtRraA and Yer010Cp from Thermus thermophilus HB8 (TtRraA) and Saccharomyces cerevisiae S288C (Yer010Cp) contain HMG aldolase and oxaloacetate decarboxylase activities and a G-X20-R-D-X2-E/D motif, that may support metal binding. The Pseudomonas putida F1 HMG/CHA aldolase has a D-X20-R-D motif. Structural and fucntional relationships of the HMG/CHA aldolase and RraA-like proteins, overview Pseudomonas putida
evolution RNase E activity A-like protein (RraA-like protein) Yer010Cp from Saccharomyces cerevisiae S288C contains HMG aldolase and oxaloacetate decarboxylase activities. The enzyme Yer010Cp contains a G-X20-R-D-X2-E/D motif Saccharomyces cerevisiae
metabolism 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases are class II pyruvate aldolases from the meta cleavage pathways of protocatechuate and gallate Pseudomonas putida
additional information the Pseudomonas putida F1 HMG/CHA aldolase has a D-X20-R-D motif, active site structure, structure-function relationship, overview. The Glu199 residue in HMG/CHA aldolase positions one water molecule and in concert with the Asp102 residue positions a second water molecule that coordinate with the bound magnesium ion Pseudomonas putida

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
86
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida
210
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
2400
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
83000
-
4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida