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Literature summary extracted from

  • Shin, I.; Percudani, R.; Rhee, S.
    Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana (2012), J. Biol. Chem., 287, 18796-18805.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.116 recombinant expression of wild-type seleno-L-methionine-substituted, N-terminally His-tagged enzyme and enzyme mutants in Escherichia coli strain BL21(DE3) Arabidopsis thaliana
3.5.3.26 expressed in Escherichia coli B834 and BL21 (DE3) cells Arabidopsis thaliana

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.116 seleno-L-methionine-substituted wild-type or N-terminally truncated mutant enzymes, hanging drop vapor diffusion method, mixing of 10 mg/ml protein in 50 mM Tris, pH 7.4, 1 mM MnCl2, and 5 mM DTT, with crystallization solution containing 0.1 M phosphate citrate, pH 4.2, 10% w/v PEG 3000, 0.2 M NaCl or with 0.1 M HEPES, pH 7.5, 7% w/v PEG 8000, 8% v/v ethylene glycol, 22°C, X-ray diffraction structure determination and analysis at 3.30 A resolution, molecular replacement, molecular modeling Arabidopsis thaliana
3.5.3.26 seleno-L-methionine-labelled enzyme, hanging drop vapor diffusion method, using either 0.1 M phosphate citrate, pH 4.2, 10% (w/v) PEG 3000, 0.2 M NaCl or 0.1 M HEPES, pH 7.5, 7% (w/v) PEG 8000, 8% (v/v) ethylene glycol Arabidopsis thaliana

Protein Variants

EC Number Protein Variants Comment Organism
3.5.1.116 E235A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 E235Q site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 H237A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 H241A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 K291A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 Q275A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 Y287A site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.1.116 Y287F site-directed mutagenesis, inactive mutant Arabidopsis thaliana
3.5.3.26 E235A inactive Arabidopsis thaliana
3.5.3.26 E235Q inactive Arabidopsis thaliana
3.5.3.26 H237A inactive Arabidopsis thaliana
3.5.3.26 H241A inactive Arabidopsis thaliana
3.5.3.26 K291A inactive Arabidopsis thaliana
3.5.3.26 K291R the mutant shows reduced activity compared to the wild type Arabidopsis thaliana
3.5.3.26 Q275A inactive Arabidopsis thaliana
3.5.3.26 Y252F the mutant shows reduced activity compared to the wild type Arabidopsis thaliana
3.5.3.26 Y287A inactive Arabidopsis thaliana
3.5.3.26 Y287F inactive Arabidopsis thaliana

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.116 1.77
-
 (S)-ureidoglycolate pH 7.4, 30°C, wild-type enzyme Arabidopsis thaliana
3.5.1.116 2.3
-
 (S)-ureidoglycolate pH 7.4, 30°C, Y252F Arabidopsis thaliana
3.5.1.116 3.46
-
 (S)-ureidoglycolate pH 7.4, 30°C, K291R Arabidopsis thaliana
3.5.3.26 1.77
-
 (S)-2-ureidoglycine wild type enzyme, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 2.3
-
 (S)-2-ureidoglycine mutant enzyme Y252F, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 3.46
-
 (S)-2-ureidoglycine mutant enzyme K291R, at pH 8.5 and 30°C Arabidopsis thaliana

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
3.5.1.116 endoplasmic reticulum
-
 Arabidopsis thaliana 5783
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.116 Mn2+ substrate (S)-ureidoglycine is bound to the Mn2+ ion at the active site of homooctameric enzyme. The Mn2+ ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction Arabidopsis thaliana
3.5.3.26 Mn2+ contains Mn2+, the Mn2+ ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction Arabidopsis thaliana

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.5.1.116 30200
-
 8 * 30200, SDS-PAGE, an octameric functional unit Arabidopsis thaliana
3.5.1.116 200000
-
 above, gel filtration Arabidopsis thaliana
3.5.3.26 30200
-
 8 * 30200, SDS-PAGE Arabidopsis thaliana
3.5.3.26 200000
-
 gel filtration Arabidopsis thaliana

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.3.26 (S)-2-ureidoglycine + H2O Arabidopsis thaliana
-
 (S)-ureidoglycolate + NH3
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.116 Arabidopsis thaliana Q8VXY9
-
-
3.5.3.26 Arabidopsis thaliana Q8GXV5
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.116 recombinant seleno-L-methionine-substituted, N-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by immobilized metal affinity chromatography, tag cleavage by TEV protease, followed by dialysis and gel filtration Arabidopsis thaliana
3.5.3.26 immobilized metal affinity column chromatography and Superdex 200 gel filtration Arabidopsis thaliana

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.116 (S)-ureidoglycolate + H2O substrate (S)-ureidoglycine is bound to the Mn2+ ion at the active site of homooctameric enzyme, conversion of (S)-ureidoglycine into (S)-ureidoglycolate in an enantioselective manner, binding mode, overview Arabidopsis thaliana glyoxylate + 2 NH3 + CO2
-
 ?
3.5.3.26 (S)-2-ureidoglycine + H2O
-
 Arabidopsis thaliana (S)-ureidoglycolate + NH3
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.116 homooctamer 8 * 30200, SDS-PAGE, an octameric functional unit Arabidopsis thaliana
3.5.1.116 More the monomer structure is in the bicupin fold of the beta-barrel Arabidopsis thaliana
3.5.3.26 homooctamer 8 * 30200, SDS-PAGE Arabidopsis thaliana

Synonyms

EC Number Synonyms Comment Organism
3.5.1.116 (S)-ureidoglycine aminohydrolase
-
 Arabidopsis thaliana
3.5.1.116 UGLYAH
-
 Arabidopsis thaliana
3.5.3.26 UGLYAH
-
 Arabidopsis thaliana

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.116 30
-
 assay at Arabidopsis thaliana

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.116 73
-
 (S)-ureidoglycolate pH 7.4, 30°C, Y252F Arabidopsis thaliana
3.5.1.116 493
-
 (S)-ureidoglycolate pH 7.4, 30°C, K291R Arabidopsis thaliana
3.5.1.116 761
-
 (S)-ureidoglycolate pH 7.4, 30°C, wild-type enzyme Arabidopsis thaliana
3.5.3.26 73
-
 (S)-2-ureidoglycine mutant enzyme Y252F, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 493
-
 (S)-2-ureidoglycine mutant enzyme K291R, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 761
-
 (S)-2-ureidoglycine wild type enzyme, at pH 8.5 and 30°C Arabidopsis thaliana

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.116 7.4
-
 assay at Arabidopsis thaliana

General Information

EC Number General Information Comment Organism
3.5.1.116 metabolism (S)-ureidoglycine aminohydrolase plays a key role in the ureide pathway of purine catabolism of plants and some bacteria Arabidopsis thaliana
3.5.1.116 additional information the Mn2+ ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. Kinetic analysis characterizes the functional roles of the active site residues, including the Mn2+ ion binding site and residues in the vicinity of (S)-ureidoglycine, structure of the enzyme and its possible catalytic mechanism, overview. The crystal structure of monomeric AtUGlyAH, which contains the ordered residues Pro39 to Leu298, is composed of 19 beta-strands and 4 short 310-helices. Residues Tyr287 and Lys291 are essential for enzyme activity, possibly by dictating the orientation of the ureido and carboxyl groups of the substrate, respectively Arabidopsis thaliana

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.116 32
-
 (S)-ureidoglycolate pH 7.4, 30°C, Y252F Arabidopsis thaliana
3.5.1.116 143
-
 (S)-ureidoglycolate pH 7.4, 30°C, K291R Arabidopsis thaliana
3.5.1.116 429
-
 (S)-ureidoglycolate pH 7.4, 30°C, wild-type enzyme Arabidopsis thaliana
3.5.3.26 32
-
 (S)-2-ureidoglycine mutant enzyme Y252F, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 143
-
 (S)-2-ureidoglycine mutant enzyme K291R, at pH 8.5 and 30°C Arabidopsis thaliana
3.5.3.26 429
-
 (S)-2-ureidoglycine wild type enzyme, at pH 8.5 and 30°C Arabidopsis thaliana