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Literature summary for 3.5.99.10 extracted from
- Crystal structures of RidA, an important enzyme for the prevention of toxic side products (2016), Sci. Rep., 6, 30494 .
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant enzyme RidA in the apo form, as well as RidA complexed with pyruvate, sitting drop vapor diffusion method, crystallization from reservoir solution containing 18% PEG 3350, 0.1 M MES, pH 6.0, 25°C, 10 days, soaking of apo-crystals in 20 mM pyruvate for 1 hour, X-ray diffraction structure determination and analysis at 2.3 A resolution | Arabidopsis thaliana |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| E180A | site-directed mutagenesis, the mutant shows moderately reduced activity compared to wild-type | Arabidopsis thaliana |
| E182A | site-directed mutagenesis, the mutation does not significantly reduce the stability of AtRidA. The mutant shows moderately reduced activity compared to wild-type | Arabidopsis thaliana |
| K136A | site-directed mutagenesis, the mutation does not significantly reduce the stability of AtRidA. Mutant K136A severely impacts the assembly, which underscores the indispensable role of the K136-E182 salt bridge as well as the inter-subunit hydrogen bonds in maintaining the oligomeric state. The mutant shows highly reduced activity compared to wild-type | Arabidopsis thaliana |
| K136R | site-directed mutagenesis, the mutation does not significantly reduce the stability of AtRidA. The mutant shows highly reduced activity compared to wild-type | Arabidopsis thaliana |
| R165A | site-directed mutagenesis, the mutation shows 98% reduced activity compared to wild-type. The mutant shows moderately reduced activity compared to wild-type | Arabidopsis thaliana |
| S166A | site-directed mutagenesis, the mutation does not significantly reduce the stability of AtRidA. The mutant shows moderately reduced activity compared to wild-type | Arabidopsis thaliana |
| S80A | site-directed mutagenesis, the mutation does not significantly reduce the stability of AtRidA. The mutant shows moderately reduced activity compared to wild-type | Arabidopsis thaliana |
| S92A | site-directed mutagenesis, the mutation does reduce the stability of AtRidA and the mutant protein is prone to precipitation | Arabidopsis thaliana |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| chloroplast | - |
Arabidopsis thaliana | 9507 | - |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 40000 | - |
recombinant enzyme, gel filtration | Arabidopsis thaliana |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Arabidopsis thaliana | Q94JQ4 | - |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | a pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with residues R165 and T167. The enzyme reduces semicarbazone formation | Arabidopsis thaliana | ? | - |
- |
 |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| homotrimer | RidA forms the trimeric, barrel-like quaternary structure and intersubunit cavities, and resembles most RidA family members. RidA exists as a homotrimer not only in crystals, but also in solution. There is a central cavity in the barrel-like trimeric structure, whose height is about A. The inner side of the barrel is formed by the beta-sheet from each monomer, and the bottom is sealed by the Q169-K178 loop. The alpha-helices pack on the outside of the barrel, while the beta-strands are approximately parallel to the 3fold crystallographic axis. The buried surface between the neighboring monomers is 1306.2 A2 | Arabidopsis thaliana |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| AtRidA | - |
Arabidopsis thaliana |
| reactive intermediate deaminase A | - |
Arabidopsis thaliana |
| ridA | - |
Arabidopsis thaliana |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8.7 | - |
assay at | Arabidopsis thaliana |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| additional information | RidA is a cofactor-independent deaminase | Arabidopsis thaliana |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | RidA forms the trimeric, barrel-like quaternary structure and intersubunit cavities, and resembles most RidA family members | Arabidopsis thaliana |
| additional information | two serine residues, S80 and S92 are involved in hydrogen-bonding interactions with the backbone nitrogens of S162 and R165 respectively | Arabidopsis thaliana |
| physiological function | RidA is an important enzyme for the prevention of toxic side products. By deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). By converting the reactive enamine/imines to harmless 2-oxoacids, RidA preempts damage to BCAT3 and ensures that the isoleucine biosynthesis can proceed | Arabidopsis thaliana |
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Release 2023.1 (January 2023)
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