Structural basis of human PRPS2 filaments

Abstract

Background PRPP synthase (PRPS) transfers the pyrophosphate groups from ATP to ribose-5-phosphate to produce 5-phosphate ribose-1-pyrophosphate (PRPP), a key intermediate in the biosynthesis of several metabolites including nucleotides, dinucleotides and some amino acids. There are three PRPS isoforms encoded in human genome. While human PRPS1 (hPRPS1) and human PRPS2 (hPRPS2) are expressed in most tissues, human PRPS3 (hPRPS3) is exclusively expressed in testis. Although hPRPS1 and hPRPS2 share 95% sequence identity, hPRPS2 has been shown to be less sensitive to allosteric inhibition and specifically upregulated in certain cancers in the translational level. Recent studies demonstrate that PRPS can form a subcellular compartment termed the cytoophidium in multiple organisms across prokaryotes and eukaryotes. Forming filaments and cytoophidia is considered as a distinctive mechanism involving the polymerization of the protein. Previously we solved the filament structures of Escherichia coli PRPS (ecPRPS) using cryo-electron microscopy (cryo-EM) 1. Results Order to investigate the function and molecular mechanism of hPRPS2 polymerization, here we solve the polymer structure of hPRPS2 at 3.08 Å resolution. hPRPS2 hexamers stack into polymers in the conditions with the allosteric/competitive inhibitor ADP. The binding modes of ADP at the canonical allosteric site and at the catalytic active site are clearly determined. A point mutation disrupting the inter-hexamer interaction prevents hPRPS2 polymerization and results in significantly reduced catalytic activity. Conclusion Findings suggest that the regulation of hPRPS2 polymer is distinct from ecPRPS polymer and provide new insights to the regulation of hPRPS2 with structural basis.

Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants

“…More than 20 different metabolic enzymes form filaments in cells, suggesting that filament assembly is a general mechanism for regulating multiple metabolic pathways (Hvorecny and Kollman, 2023; Lynch et al, 2020; Narayanaswamy et al, 2009; Noree et al, 2010; Park and Horton, 2019; Park and Horton, 2020; Shen et al, 2016; Simonet et al, 2020). For many metabolic enzymes, filament formation is an important mechanism for fine-tuning catalytic activity (Barry et al, 2014; Hansen et al, 2021; Hu et al, 2022; Hunkeler et al, 2018; Hvorecny et al, 2023; Lu et al, 2023; Lynch and Kollman, 2020; Lynch et al, 2017; Polley et al, 2019; Stoddard et al, 2020; Zhong et al, 2022). Here, we demonstrate that filament assembly itself can be directly tuned by phosphorylation, adding an additional layer to an already complex mode of regulation for IMPDH that occurs at different levels.…”

Regulatory mechanism and expression level of PRPS2 in lung cancer

“…Phosphoribosyl pyrophosphate synthetase (PRPS) is a key rate-limiting enzyme in nucleotide synthesis, containing three subtypes: PRPS1, PRPS2, and PRPS3. 7 It has been Zhenzhen Chen and Lei Wei contributed equally to the study.…”

“…Phosphoribosyl pyrophosphate synthetase (PRPS) is a key rate‐limiting enzyme in nucleotide synthesis, containing three subtypes: PRPS1, PRPS2, and PRPS3. 7 It has been found that PRPS1 and PRPS2 play important regulatory roles in different malignant tumors. PRPS1 is overexpressed in melanoma and accelerates tumor progression by promoting cell growth, metastasis, and suppressing cell apoptosis.…”