Literature summary for 3.5.2.2 extracted from

Cheng, J.H.; Huang, C.C.; Huang, Y.H.; Huang, C.Y.
Structural basis for pH-dependent oligomerization of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 (2018), Bioinorg. Chem. Appl., 2018, 9564391 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of His-tagged enzyme	Pseudomonas aeruginosa

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme, hanging drop vapor diffusion method, mixing of 20 mg/ml protein in 20 mM MES, and 100 mM NaCl, pH 5.9, with reservoir solution containing 10% PEG 8000, 100 mM HEPES, 200 mM calcium acetate, pH 5.9, at room temperature, X-ray diffraction structure determination and analysis at 2.17 A resolution. An asymmetric unit of the crystal contains four crystallographically independent dihydropyrimidinase monomers. The crystals of the dimeric Pseudomonas aeruginosa dihydropyrimidinase belong to space group P3121 grown at the condition of 28% PEG 6000, 100 mM HEPES, 200 mM lithium acetate, pH 7.5	Pseudomonas aeruginosa

Crystallization (Comment)

Organism

purified enzyme, hanging drop vapor diffusion method, mixing of 20 mg/ml protein in 20 mM MES, and 100 mM NaCl, pH 5.9, with reservoir solution containing 10% PEG 8000, 100 mM HEPES, 200 mM calcium acetate, pH 5.9, at room temperature, X-ray diffraction structure determination and analysis at 2.17 A resolution. An asymmetric unit of the crystal contains four crystallographically independent dihydropyrimidinase monomers. The crystals of the dimeric Pseudomonas aeruginosa dihydropyrimidinase belong to space group P3121 grown at the condition of 28% PEG 6000, 100 mM HEPES, 200 mM lithium acetate, pH 7.5

Pseudomonas aeruginosa

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Zn2+	a dimetalloenzyme	Pseudomonas aeruginosa

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa ATCC 15692	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa 1C	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa PRS 101	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa DSM 22644	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa CIP 104116	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa LMG 12228	-	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	Pseudomonas aeruginosa JCM 14847	-	3-ureidopropanoate	-	r

Organism

Organism	UniProt	Comment	Textmining
Pseudomonas aeruginosa	Q9I676	-	-
Pseudomonas aeruginosa 1C	Q9I676	-	-
Pseudomonas aeruginosa ATCC 15692	Q9I676	-	-
Pseudomonas aeruginosa CIP 104116	Q9I676	-	-
Pseudomonas aeruginosa DSM 22644	Q9I676	-	-
Pseudomonas aeruginosa JCM 14847	Q9I676	-	-
Pseudomonas aeruginosa LMG 12228	Q9I676	-	-
Pseudomonas aeruginosa PRS 101	Q9I676	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme by nickel affinity chromatography and dialysis to over 97% purity	Pseudomonas aeruginosa

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa ATCC 15692	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa 1C	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa PRS 101	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa DSM 22644	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa CIP 104116	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa LMG 12228	3-ureidopropanoate	-	r
5,6-dihydrouracil + H2O	-	Pseudomonas aeruginosa JCM 14847	3-ureidopropanoate	-	r

Subunits

Subunits	Comment	Organism
dimer or tetramer	pH-dependent oligomerization of dihydropyrimidinase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH 7.5. Gel filtration chromatographic analysis of purified dihydropyrimidinase reveals a mixture of dimers and tetramers at pH 5.9, with mainly tetramers	Pseudomonas aeruginosa
More	Pseudomonas aeruginosa dihydropyrimidinase unit consists of 17 alpha-helices, 19 beta-sheets, and two zinc ions. The enzyme monomer consists of two domains, namely, a large domain with a classic (beta/alpha)8-barrel structure core embedding the catalytic dimetal center and a small beta-sandwich domain	Pseudomonas aeruginosa

Synonyms

Synonyms	Comment	Organism
dht	-	Pseudomonas aeruginosa

General Information

General Information	Comment	Organism
evolution	enzyme dihydropyrimidinase is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase	Pseudomonas aeruginosa
metabolism	dihydropyrimidinase is a key enzyme for pyrimidine catabolism, it catalyzes the reversible cyclization of dihydrouracil to N-carbamoyl-beta-alanine in the second step of the pyrimidine degradation pathway	Pseudomonas aeruginosa
additional information	the enzyme contains a carboxylated lysine within the active site	Pseudomonas aeruginosa
physiological function	dihydropyrimidinase can detoxify xenobiotics with an imide functional group, ranging from linear imides to heterocyclic imides. Homologous enzymes from microorganisms are known as hydantoinase, used as biocatalyst for hydrolysis of 5-monosubstituted hydantoins in the synthesis of D- and L-amino acids	Pseudomonas aeruginosa