4.1.1.23: orotidine-5'-phosphate decarboxylase

crystal structure in complex with inhibitor (5-(4-amino-3-oxido-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl)-methyl dihydrogen phosphate. Compared to cytosin, the pyrimidine portion exhibits changes in the atomic arrangement. The oxygen atom migrates from N3 to N4 or the C5 position of the cytosine ring. These rearranged nucleotides are each bound to the enzyme in a 2?-endo,syn conformation

Homo sapiens

P11172

728095

hanging drop vapor diffusion method

nine crystal structures of human OMPD in complex with substrate, product and nucleotide inhibitors are described

Homo sapiens

P11172

695160

purified detagged recombinant enzyme, 5 mg/ml protein in 20 mM HEPES-NaOH, pH 7.4, sitting-drop setup, mixing with 0.1 M Tris-HCl, pH 8.0, and 1.8 M (NH4)2SO4 in a 1:1 ratio at 22°C, cryoprotection with 20%v/v glycerol in mother liquor, X-ray diffraction structure determination and analysis at 1.85-1.92 A resolution, molecular replacement using data from a highly twinned monoclinic crystal, pseudo-merohedrally twinned crystals, overview

Homo sapiens

P11172

677324

crystal structures of hydrophobic pocket mutants I96S, I96T, L123N, L123S, V155D, and V155S in the presence of 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid or azaUMP. The interactions of the transition state/vinyl carbanion intermediate with the active site are preserved in each mutant

Methanobacterium thermoautotrophicus

726966

crystal structures with ligand anlogues. Enzyme can distort the bond between the aromatic ring of a ligand and its C6 substituent, regardless of the latter's charge or size. The distortion contributes 3.7 kcal/mol to the catalysis. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of orotidine 5'-monophosphate both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. In addition, the bond between the carboxylate group and the pyrimidine ring is distorted

727691

eight different crystal forms are grown by the sitting drop method at room temperature for single mutant enzymes liganded with 1-(5-phospho-beta-ribofuranosyl)barbituric acid: Q185A/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid], R203A/[1-(5-phospho-beta-ribofuranosyl)barbituric acid], T159V/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid], T159A/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid], T159S/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid], R160A/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid], Y206F/[1-(5-phospho-beta-ribofuranosyl)barbituric acid], K82A/[1-(5-phospho-beta-D-ribofuranosyl)barbituric acid]

727006

in complex with the inhibitor 6-azauridine 5-phosphate

651572

ligand-free ODCase form and complexed with 6-azauridine 5-phosphate

653647

mutants Q185A, R203A, T159V, T159A, T159S, R160A, Y206F, K82A, and double- and triple mutants, to 1.3-1.6 A resolution

727006

native ODCase complexed with 6-azauridine 5'-phosphate, several active site mutants complexed with a variety of ligands, including substrate, product and inhibitors

650145

with and without the inhibitor 6-azaUMP, vapour-diffusion method

649128

X-ray structure of ODCase complexed with 6-azaorotidine 5-phosphate

650934

apo, substrate or product-complex forms of OMPDC, X-ray diffraction structure determination and anaylsis at 2.65-2.7 A

680570

in complex with inhibitor 4-(2-hydroxy-4-methoxyphenyl)-4-oxobutanoic acid, to 2.1 A resolution. The inhibitor molecule occupies a part of the active site that overlaps with the phosphate-binding region in the OMP- or UMP-bound complexes. The carboxyl group of the inhibitor causes a dramatic movement of the L1 and L2 loops that play a role in the recognition of the substrate and product molecules

Q8T6J6

727794

purified recombinant enzyme, seeding method in a hanging drop, 20°C, 10 mg/ml protein in in 50 mM Tris-HCl, pH 8.0, containing 300 mM NaCl and 5 mM dithiothreitol, method optimization, X-ray diffraction structure determination and analysis at 2.7 A resolution

677396

the crystal structures of Plasmodium falciparum ODCase in complex with 6-I-UMP, 6-N3-UMP and 6-NH2-UMP are solved at resolutions of 1.95, 1.90 and 1.8 A, respectively

Q8IJH3

693558

the crystal structures of the apo form of OMPDC, and in complex with OMP and UMP are resolved at resolutions of 2.7, 2.65 and 2.65 A, respectively

680570

the structure of PfODCase is solved to a resolution of 1.5418 A

Q8T6J6

690945

4186, 649921, 649975

complexed with the inhibitor 6-hydroxyuridine 5-phosphate

P03962

650068

hanging drop vapor diffusion method, using 100 mM Tris-HCl, pH 8.4, 2.12 M ammonium sulfate (enzyme in complex with 4 and 10) or using 100 mM Tris-HCl, pH 8.4, 1.4 M ammonium sulfate (enzyme in complex with pyrazofurin-5'-monophosphate)

in complex with 6-hydroxyuridine 5-phosphate

652109

in complex with different ligands, e.g. 6-hydroxyuridine 5'-phosphate

649331

molecular dynamics simulations on X-ray structure of the enzyme in its free form as well as in complex with ligands 1-(5'-phospho-D-ribofuranosyl) barbituric acid, orotidine 5'-monophosphate, and 6-phosphonouridine 5'-monophosphate

728002

orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid

4190

PDB ID 1DQX, free enzyme and enzyme bound to 6-hydroxy-UMP, crystal structure analysis of the enzyme in presence or absence of a potenial transition state analogue, comparison to predicted structure by QM/MM enzyme simulations, overview

682233

Staphylococcus aureus