7YK1

Structural basis of human PRPS2 filaments


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of human PRPS2 filaments.

Lu, G.M.Hu, H.H.Chang, C.C.Zhong, J.Zhou, X.Guo, C.J.Zhang, T.Li, Y.L.Yin, B.Liu, J.L.

(2023) Cell Biosci 13: 100-100

  • DOI: https://doi.org/10.1186/s13578-023-01037-z
  • Primary Citation of Related Structures:  
    7YK1

  • PubMed Abstract: 

    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 . 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. 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.


  • Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase 2
A, B, C, D, E
A, B, C, D, E, F
324Homo sapiensMutation(s): 0 
Gene Names: PRPS2
EC: 2.7.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11908 (Homo sapiens)
Explore P11908 
Go to UniProtKB:  P11908
PHAROS:  P11908
GTEx:  ENSG00000101911 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11908
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
I [auth A]
J [auth A]
M [auth B]
AA [auth F],
BA [auth F],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
S [auth D],
V [auth D],
W [auth E],
X [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth F]
G [auth A]
K [auth B]
Q [auth C]
T [auth D]
CA [auth F],
G [auth A],
K [auth B],
Q [auth C],
T [auth D],
Y [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth F]
H [auth A]
L [auth B]
R [auth C]
U [auth D]
DA [auth F],
H [auth A],
L [auth B],
R [auth C],
U [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)ChinaNo. 2021YFA0804700
National Natural Science Foundation of China (NSFC)ChinaNo. 31771490

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references