8J0F

GK tetramer with adjacent hooks at reaction state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Dynamic Arabidopsis P5CS filament facilitates substrate channelling.

Guo, C.J.Zhang, T.Leng, Q.Zhou, X.Zhong, J.Liu, J.L.

(2024) Nat Plants 10: 880-889

  • DOI: https://doi.org/10.1038/s41477-024-01697-w
  • Primary Citation of Related Structures:  
    8J0F, 8Y2H

  • PubMed Abstract: 

    In plants, the rapid accumulation of proline is a common response to combat abiotic stress 1-7 . Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing the initial two-step conversion from glutamate to proline 8 . Here we determine the first structure of plant P5CS. Our results show that Arabidopsis thaliana P5CS1 (AtP5CS1) and P5CS2 (AtP5CS2) can form enzymatic filaments in a substrate-sensitive manner. The destruction of AtP5CS filaments by mutagenesis leads to a significant reduction in enzymatic activity. Furthermore, separate activity tests on two domains reveal that filament-based substrate channelling is essential for maintaining the high catalytic efficiency of AtP5CS. Our study demonstrates the unique mechanism for the efficient catalysis of AtP5CS, shedding light on the intricate mechanisms underlying plant proline metabolism and stress response.


  • 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 synthase B726Arabidopsis thalianaMutation(s): 0 
Gene Names: P5CSBP5CS2At3g55610F1I16_20
EC: 2.7.2.11 (PDB Primary Data), 1.2.1.41 (PDB Primary Data)
UniProt
Find proteins for P54888 (Arabidopsis thaliana)
Explore P54888 
Go to UniProtKB:  P54888
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54888
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 
I [auth C],
L [auth A],
O [auth B],
R [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
RGP (Subject of Investigation/LOI)
Query on RGP

Download Ideal Coordinates CCD File 
J [auth C],
M [auth A],
P [auth B],
S [auth D]
GAMMA-GLUTAMYL PHOSPHATE
C5 H10 N O7 P
PJRXVIJAERNUIP-GSVOUGTGSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
K [auth C],
N [auth A],
Q [auth B],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references