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Literature summary 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)

EC Number Cloned (Comment) Organism
4.1.3.17 phylogenetic analysis Pseudomonas putida

Protein Variants

EC Number Protein Variants Comment Organism
4.1.3.B3 E199A site-directed mutagenesis, the mutant shows reduced 4-hydroxy-4-methyl-2-oxoglutarate aldolase and oxaloacetate decarboxylase activities compared to the wild-type enzyme Pseudomonas putida
4.1.3.17 E199A site-directed mutagenesis, the mutant shows reduced activity and reduced affinity for Co2+ compared to the wild-type enzyme Pseudomonas putida

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.3.B3 oxalate competitive inhibition Pseudomonas putida
4.1.3.17 oxalate competitive inhibition Pseudomonas putida
4.1.3.17 oxalate competitive inhibition Saccharomyces cerevisiae
4.1.3.17 oxalate competitive inhibition Thermus thermophilus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.1.3.17 0.1265
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
4.1.3.17 0.1507
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
4.1.3.17 0.1876
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida
4.1.3.17 0.7086
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.3.B3 Co2+ required Pseudomonas putida
4.1.3.B3 Mg2+ a magnesium ion is coordinated directly or indirectly via water through interactions with Asp102, Asp124, and Glu199 Pseudomonas putida
4.1.3.B3 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
4.1.3.17 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
4.1.3.17 Co2+ required, equally activating as Ni2+ Thermus thermophilus
4.1.3.17 Mg2+ a magnesium ion is coordinated directly or indirectly via water through interactions with Asp102, Asp124, and Glu199 Pseudomonas putida
4.1.3.17 additional information the enzyme is a class II divalent metal ion-dependent aldolase Thermus thermophilus
4.1.3.17 additional information the enzyme is a class II divalent metal ion-dependent aldolase Saccharomyces cerevisiae
4.1.3.17 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
4.1.3.17 Ni2+ required, best activating metal ion Saccharomyces cerevisiae
4.1.3.17 Ni2+ required, equally activating as Co2+ Thermus thermophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.3.B3 4-carboxy-4-hydroxy-2-oxoadipate Pseudomonas putida
-
 oxaloacetate + pyruvate
-
 ?
4.1.3.B3 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. EC 4.1.3.17. 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 ?
-
 ?
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate Pseudomonas putida
-
 2 pyruvate
-
 ?
4.1.3.17 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

EC Number Organism UniProt Comment Textmining
4.1.3.B3 Pseudomonas putida A5W059
-
-
4.1.3.17 Pseudomonas putida
-
-
-
4.1.3.17 Saccharomyces cerevisiae
-
-
-
4.1.3.17 Thermus thermophilus
-
-
-
4.1.3.17 Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.3.B3 4-carboxy-4-hydroxy-2-oxoadipate
-
 Pseudomonas putida oxaloacetate + pyruvate
-
 ?
4.1.3.B3 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. EC 4.1.3.17. 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 ?
-
 ?
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate
-
 Thermus thermophilus 2 pyruvate
-
 ?
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate
-
 Saccharomyces cerevisiae 2 pyruvate
-
 ?
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate
-
 Pseudomonas putida 2 pyruvate
-
 ?
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate
-
 Thermus thermophilus HB8 / ATCC 27634 / DSM 579 2 pyruvate
-
 ?
4.1.3.17 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 ?
-
 ?
4.1.3.17 additional information the RNAse E activity A-like protein TtRraA from Thermus thermophilus HB8 contains HMG aldolase and oxaloacetate decarboxylase activities Thermus thermophilus ?
-
 ?
4.1.3.17 additional information the RNAse E activity A-like protein Yer010Cp from Saccharomyces cerevisiae S288C contains HMG aldolase and oxaloacetate decarboxylase activities Saccharomyces cerevisiae ?
-
 ?
4.1.3.17 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

EC Number Subunits Comment Organism
4.1.3.B3 trimer
-
 Pseudomonas putida
4.1.3.17 trimer
-
 Pseudomonas putida

Synonyms

EC Number Synonyms Comment Organism
4.1.3.B3 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase
-
 Pseudomonas putida
4.1.3.B3 CHA aldolase
-
 Pseudomonas putida
4.1.3.B3 HMG/CHA aldolase
-
 Pseudomonas putida
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate aldolase
-
 Pseudomonas putida
4.1.3.17 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase
-
 Pseudomonas putida
4.1.3.17 HMG aldolase
-
 Thermus thermophilus
4.1.3.17 HMG aldolase
-
 Saccharomyces cerevisiae
4.1.3.17 HMG aldolase
-
 Pseudomonas putida
4.1.3.17 HMG/CHA aldolase
-
 Pseudomonas putida

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.1.3.17 25
-
 assay at Thermus thermophilus
4.1.3.17 25
-
 assay at Saccharomyces cerevisiae
4.1.3.17 25
-
 assay at Pseudomonas putida

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.3.17 0.0276
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
4.1.3.17 0.061
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida
4.1.3.17 0.356
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
4.1.3.17 15.6
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.1.3.17 8
-
 assay at Thermus thermophilus
4.1.3.17 8
-
 assay at Saccharomyces cerevisiae
4.1.3.17 8
-
 assay at Pseudomonas putida

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
4.1.3.17 0.0319
-
 oxalate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
4.1.3.17 0.0377
-
 oxalate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus

General Information

EC Number General Information Comment Organism
4.1.3.B3 evolution structural and functional relationships of the HMG/CHA aldolase and RraA-like proteins, overview Pseudomonas putida
4.1.3.B3 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. The enzyme catalyzes the final step Pseudomonas putida
4.1.3.B3 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
4.1.3.17 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
4.1.3.17 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
4.1.3.17 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
4.1.3.17 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
4.1.3.17 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
4.1.3.17 86
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, mutant E199A Pseudomonas putida
4.1.3.17 210
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein Yer010Cp Saccharomyces cerevisiae
4.1.3.17 2400
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, RraA-like protein TtRraA Thermus thermophilus
4.1.3.17 83000
-
 4-hydroxy-4-methyl-2-oxoglutarate pH 8.0, 25°C, wild-type enzyme Pseudomonas putida