8YPZ image
Deposition Date 2024-03-18
Release Date 2025-03-19
Last Version Date 2025-10-08
Entry Detail
PDB ID:
8YPZ
Title:
Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.31
R-Value Work:
0.26
Space Group:
P 65
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribose-phosphate pyrophosphokinase 1
Gene (Uniprot):PRPS1
Chain IDs:A, B, C, D, E, F
Chain Length:318
Number of Molecules:6
Biological Source:Homo sapiens
Primary Citation
PRPS2 enhances RNA m 6 A methylation by stimulating SAM synthesis through enzyme-dependent and independent mechanisms.
Nat Commun 16 3966 3966 (2025)
PMID: 40295500 DOI: 10.1038/s41467-025-59119-0

Abstact

Cancer cells exploit altered metabolic pathways to dynamically regulate epigenetic methylation and thus promote tumorigenesis and metastasis. In various human cancers, such as lung adenocarcinoma, the level of a key cellular metabolite, S-adenosylmethionine (SAM), is prominently upregulated for RNA hypermethylation as the methyl donor. However, the specific mechanisms by which cancer cells produce SAM to sustain RNA methylation remain elusive. Here, we demonstrate that PRPS2, a phosphoribosyl pyrophosphate synthetase isoform involved in the first and rate-limiting step of the purine biosynthesis pathway, exhibits distinct oncogenic functionality in regulating RNA methylation, unlike its homolog PRPS1. PRPS2 utilizes four non-conserved key residues to bypass the typical ADP/GDP allosteric feedback inhibition, enabling sustained excess production of newly synthesized ATP. Moreover, PRPS2 stabilizes methionine adenosyltransferase 2 A (MAT2A) through direct interactions to positively stimulate ATP utilization and SAM synthesis for RNA m6A specific methylation via the WTAP/METTL3/METTL14 methyltransferase complex, thereby promoting lung tumorigenesis. Our study links nucleotide biosynthesis with RNA epigenetics in cancer progression through the PRPS2-MAT2A-WTAP/METTL3/METTL14 axis, and elucidates both enzyme-dependent and independent functions of PRPS2. These findings have significant implications for developing targeted therapies for cancers associated with PRPS2 abnormalities.

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Primary Citation of related structures