7XMU

E.coli phosphoribosylpyrophosphate (PRPP) synthetase type A filament bound with ADP, Pi and R5P


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 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

Filamentation modulates allosteric regulation of PRPS.

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

(2022) Elife 11

  • DOI: 10.7554/eLife.79552
  • Primary Citation of Related Structures:  
    7XMU, 7XMV, 7XN3

  • PubMed Abstract: 
  • Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis ...

    Phosphoribosyl pyrophosphate (PRPP) is a key intermediate in the biosynthesis of purine and pyrimidine nucleotides, histidine, tryptophan, and cofactors NAD and NADP. Abnormal regulation of PRPP synthase (PRPS) is associated with human disorders, including Arts syndrome, retinal dystrophy, and gouty arthritis. Recent studies have demonstrated that PRPS can form filamentous cytoophidia in eukaryotes. Here, we show that PRPS forms cytoophidia in prokaryotes both in vitro and in vivo. Moreover, we solve two distinct filament structures of E. coli PRPS at near-atomic resolution using Cryo-EM. The formation of the two types of filaments is controlled by the binding of different ligands. One filament type is resistant to allosteric inhibition. The structural comparison reveals conformational changes of a regulatory flexible loop, which may regulate the binding of the allosteric inhibitor and the substrate ATP. A noncanonical allosteric AMP/ADP binding site is identified to stabilize the conformation of the regulatory flexible loop. Our findings not only explore a new mechanism of PRPS regulation with structural basis, but also propose an additional layer of cell metabolism through PRPS filamentation.


    Organizational Affiliation

    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase321Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: prsprsAb1207JW1198
EC: 2.7.6.1
UniProt
Find proteins for P0A717 (Escherichia coli (strain K12))
Explore P0A717 
Go to UniProtKB:  P0A717
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A717
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
DA [auth E],
EA [auth E],
JA [auth F],
K [auth A],
L [auth A],
DA [auth E],
EA [auth E],
JA [auth F],
K [auth A],
L [auth A],
M [auth A],
OA [auth C],
PA [auth C],
R [auth D],
S [auth D],
X [auth B],
Y [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
HSX (Subject of Investigation/LOI)
Query on HSX

Download Ideal Coordinates CCD File 
FA [auth F],
G [auth A],
KA [auth C],
N [auth D],
T [auth B],
FA [auth F],
G [auth A],
KA [auth C],
N [auth D],
T [auth B],
Z [auth E]
5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
 Ligand Interaction
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
BA [auth E],
HA [auth F],
I [auth A],
MA [auth C],
P [auth D],
BA [auth E],
HA [auth F],
I [auth A],
MA [auth C],
P [auth D],
V [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E],
CA [auth E],
GA [auth F],
H [auth A],
IA [auth F],
AA [auth E],
CA [auth E],
GA [auth F],
H [auth A],
IA [auth F],
J [auth A],
LA [auth C],
NA [auth C],
O [auth D],
Q [auth D],
U [auth B],
W [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 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. 2021YFA0804701-4
National Natural Science Foundation of China (NSFC)ChinaNo. 31771490

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references