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Ureidoglycolate lyase (UGL, EC 4.3.2.3) catalyzes the breakdown of ureidoglycolate to glyoxylate and urea, which is the final step in the catabolic pathway leading from purines to urea. Although the sequence of enzymatic steps was worked out nearly 40 years ago, the stereochemistry of the uric acid degradation pathway and the catalytic properties of UGL have remained very poorly described. We now report the first direct investigation of the absolute stereochemistry of UGL catalysis. Using chiral chromatographic analyses with substrate enantiomers, we demonstrate that UGL catalysis is stereospecific for substrates with the (S)-hydroxyglycine configuration. The first potent competitive inhibitors for UGL are reported here. These inhibitors are compounds which contain a 2,4-dioxocarboxylate moiety, designed to mimic transient species produced during lyase catalysis. The most potent inhibitor, 2,4-dioxo-4-phenylbutanoic acid, exhibits a K I value of 2.2 nM and is therefore among the most potent competitive inhibitors ever reported for a lyase enzyme. New synthetic alternate substrates for UGL, which are acyl-␣-hydroxyglycine compounds, are described. Based on these alternate substrates, we introduce the first assay method for monitoring UGL activity directly. Finally, we report the first putative primary nucleotide and derived peptide sequence for UGL. This sequence exhibits a high level of similarity to the fumarylacetoacetate hydrolase family of proteins. Close mechanistic similarities can be visualized between the chemistries of ureidoglycolate lyase and fumarylacetoacetate hydrolase catalysis.Ureidoglycolate lyase (UGL, 1 EC 4.3.2.3) and allantoicase (Acase, EC 3.5.3.4) are the enzymes that catalyze the final steps in the catabolic pathway leading from purines to urea. In this pathway ( Fig. 1), allantoic acid is formed from allantoin by allantoinase, Acase then converts allantoic acid to ureidoglycolate and urea, and, finally, UGL catalyzes the breakdown of ureidoglycolate to glyoxylate and urea. Acase was first found independently in frog liver by Krebs and Weil (1) and in the mycelium of Aspergillus niger by Brunel (2). UGL was first described by Valentine et al. (3,4) in Streptococcus allantoicus and in a strain of Pseudomonas. It has since been established that UGL and Acase are both functional in many bacteria, yeast, fish, and rat (5-16), whereas in some species only one of these activities has been detected (2, 17-23).The stereochemistry of UGL catalysis, and indeed of the uric acid degradation pathway as a whole, has remained poorly described for many years. Conflicting results have been reported as to whether UGL reacts preferentially with (Ϫ)-ureidoglycolate (5, 6, 9, 10, 18) or with (ϩ)-ureidoglycolate (17). Moreover, allantoinase reacts with both enantiomers of allantoin, and Acase has been reported to produce ureidoglycolate exhibiting a negative rotation, but, paradoxically, to also convert ureidoglycolate exhibiting a positive rotation to glyoxylate and urea (11). Thus, the stereospecificity of U...

The nucleotide sequence data for yeast mitochondrial ribosomal protein (MRP) genes were analyzed by the computer program GeneMark which predicts the presence of likely genes in sequence data by calculating statistical biases in the appearance of consecutive nucleotides. The program uses a set of standard sequence data for this calculation. We used this program for the analysis of yeast nucleotide sequence data containing MRP genes, hoping to obtain information as to whether they share features in common that are different from other yeast genes. Sequence data sets for ordinary yeast genes and for 27 known MRP genes were used. The MRP genes were nicely predicted as likely genes regardless of the data sets used, whereas other yeast genes were predicted to be likely genes only when the data set for ordinary yeast genes was used. The assembled sequence data for chromosomes II, III, VIII and XI as well as the segmented data for chromosome V were analyzed in a similar manner. In addition to the known MRP genes, eleven ORF's were predicted to be likely MRP genes. Thus, the method seems very powerful in analyzing genes of heterologous origins.