7WXG

GPR domain closed form of Drosophila P5CS filament with glutamate, ATP, and NADPH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of dynamic P5CS filaments.

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

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.76107
  • Primary Citation of Related Structures:  
    7F5T, 7F5U, 7F5V, 7F5X, 7WX3, 7WX4, 7WXF, 7WXG, 7WXH, 7WXI

  • PubMed Abstract: 

    The bifunctional enzyme Δ 1 -pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations in the P5CS gene (ALDH18A1) lead to neurocutaneous syndrome and skin relaxation connective tissue disease in humans, and P5CS deficiency seriously damages the ability to resist adversity in plants. We have recently found that P5CS forms cytoophidia in vivo and filaments in vitro. However, it is difficult to appreciate the function of P5CS filamentation without precise structures. Using cryo-electron microscopy, here we solve the structures of Drosophila full-length P5CS in three states at resolution from 3.1 to 4.3 Å. We observe distinct ligand-binding states and conformational changes for the GK and GPR domains, respectively. Divergent helical filaments are assembled by P5CS tetramers and stabilized by multiple interfaces. Point mutations disturbing those interfaces prevent P5CS filamentation and greatly reduce the enzymatic activity. Our findings reveal that filamentation is crucial for the coordination between the GK and GPR domains, providing a structural basis for the catalytic function of P5CS filaments.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-1-pyrroline-5-carboxylate synthase776Drosophila melanogasterMutation(s): 0 
Gene Names: P5CSDmel\CG7470CG7470Dmel_CG7470
EC: 2.7.2.11 (PDB Primary Data), 1.2.1.41 (PDB Primary Data)
UniProt
Find proteins for Q9VNW6 (Drosophila melanogaster)
Explore Q9VNW6 
Go to UniProtKB:  Q9VNW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VNW6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Structure summary
  • Version 1.2: 2024-06-26
    Changes: Data collection