8YPZ | pdb_00008ypz

Crystal strcture of human phosphoribosyl pyrophosphate synthetase 1 (PRPS1) in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.310 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.283 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

PRPS2 enhances RNA m 6 A methylation by stimulating SAM synthesis through enzyme-dependent and independent mechanisms.

Zhang, L.Zhao, X.Hu, J.Li, T.Chen, H.Z.Zhang, A.Wang, H.Yu, J.Zhang, L.

(2025) Nat Commun 16: 3966-3966

  • DOI: https://doi.org/10.1038/s41467-025-59119-0
  • Primary Citation of Related Structures:  
    8YPY, 8YPZ, 8YQ0

  • PubMed Abstract: 

    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 m 6 A 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.


  • Organizational Affiliation
    • Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase 1
A, B, C, D, E
A, B, C, D, E, F
318Homo sapiensMutation(s): 0 
Gene Names: PRPS1
EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60891 (Homo sapiens)
Explore P60891 
Go to UniProtKB:  P60891
PHAROS:  P60891
GTEx:  ENSG00000147224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60891
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
G [auth A]
K [auth A]
M [auth B]
P [auth C]
U [auth D]
G [auth A],
K [auth A],
M [auth B],
P [auth C],
U [auth D],
X [auth E]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
AA [auth F]
I [auth A]
J [auth A]
R [auth C]
S [auth C]
AA [auth F],
I [auth A],
J [auth A],
R [auth C],
S [auth C],
Z [auth E]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
HSX
Query on HSX

Download Ideal Coordinates CCD File 
BA [auth F],
H [auth A],
N [auth B],
Q [auth C],
Y [auth E]
5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth F]
L [auth A]
O [auth B]
T [auth C]
V [auth D]
CA [auth F],
L [auth A],
O [auth B],
T [auth C],
V [auth D],
W [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.310 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.283 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.876α = 90
b = 186.876β = 90
c = 160.641γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22077081

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references