The 3-ureidopropionase of Caenorhabditis elegans, an enzyme involved in pyrimidine degradation

Identification of Biomarkers of Sepsis-Associated Acute Kidney Injury in Pediatric Patients Based on UPLC-QTOF/MS

Sepsis or septic shock is often accompanied by organ dysfunction, among which acute kidney injury (AKI) is the most frequent event that appears early during sepsis. To harness urinary metabolic profiling to discover potential biomarkers of septic acute kidney injury in pediatric patients at intensive care units, we collected urine samples from 27 septic children with AKI and 30 septic children without AKI. We used ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) for profiling and multiple regression analysis to explore the potential biomarkers of sepsis with AKI. We identified a clear distinction in the UPLC-QTOF/MS results for septic children with and without AKI after the development of sepsis, specifically 18 and 17 metabolites with different levels at 12 and 24 h, respectively. Metabolic pathways associated with septic AKI included lipid metabolism, particularly processes involving glycerophospholipid metabolism. L-Histidine, DL-indole-3-lactic acid, trimethylamine N-oxide, and caprylic acid were uncovered as potential biomarkers of septic AKI at 12 h, while gentisaldehyde, 3-ureidopropionate, N4-acetylcytidine, and 3-methoxy-4-hydroxyphenylglycol sulfate were identified as potential candidates at 24 h. We further found that combinations of metabolites were more effective diagnostic marker compared with individual metabolites, with an area under the receiver operating characteristics curve of 0.905 and 0.97 at 12 and 24 h, respectively. Our results indicated that metabolomic analysis could be a promising approach for identifying diagnostic biomarkers of pediatric septic AKI and helped elucidate the pathological mechanisms involved.

Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism

β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer-dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer-dimer interface, effectively positioning the catalytically important Glu207 in the active site.