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- PDB-8y2h: GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state -

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Basic information

Entry
Database: PDB / ID: 8y2h
TitleGK tetramer of AtP5CS1 filament with adjacent hooks, reaction state
ComponentsDelta-1-pyrroline-5-carboxylate synthase A
KeywordsPLANT PROTEIN / L-proline biosynthesis / filamentous enzyme / TRANSFERASE
Function / homology
Function and homology information


delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / hyperosmotic salinity response / pollen development / root development / L-proline biosynthetic process / proline biosynthetic process ...delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / hyperosmotic salinity response / pollen development / root development / L-proline biosynthetic process / proline biosynthetic process / response to water deprivation / response to salt stress / chloroplast / response to oxidative stress / Golgi apparatus / ATP binding / cytoplasm
Similarity search - Function
Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily ...Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Delta-1-pyrroline-5-carboxylate synthase A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang, T. / Guo, C.J. / Liu, J.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2024
Title: Dynamic Arabidopsis P5CS filament facilitates substrate channelling.
Authors: Chen-Jun Guo / Tianyi Zhang / Qingqing Leng / Xian Zhou / Jiale Zhong / Ji-Long Liu /
Abstract: In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing ...In plants, the rapid accumulation of proline is a common response to combat abiotic stress. 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. 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.
History
DepositionJan 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Delta-1-pyrroline-5-carboxylate synthase A
A: Delta-1-pyrroline-5-carboxylate synthase A
F: Delta-1-pyrroline-5-carboxylate synthase A
C: Delta-1-pyrroline-5-carboxylate synthase A
G: Delta-1-pyrroline-5-carboxylate synthase A
D: Delta-1-pyrroline-5-carboxylate synthase A
H: Delta-1-pyrroline-5-carboxylate synthase A
E: Delta-1-pyrroline-5-carboxylate synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)633,97312
Polymers631,9458
Non-polymers2,0294
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate synthase A / P5CS A


Mass: 78993.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: P5CSA, P5CS1, At2g39800, T5I7.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: P54887, glutamate 5-kinase, glutamate-5-semialdehyde dehydrogenase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana P5CSA incubated with all substrates.
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 78.9 kDa/nm / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487:model refinement
13cryoSPARC4.4.03D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222855 / Symmetry type: POINT
RefinementCross valid method: NONE

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