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- PDB-7f5t: Drosophila P5CS filament with glutamate -

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Basic information

Entry
Database: PDB / ID: 7f5t
TitleDrosophila P5CS filament with glutamate
ComponentsDelta-1-pyrroline-5-carboxylate synthase
KeywordsTRANSFERASE / glutamate-bound / filament / ALDH18A1 / Delta-1-pyrroline-5-carboxylate synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Mitochondrial protein degradation / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / mitochondrion / ATP binding
Similarity search - Function
Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / 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 ...Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / 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
GLUTAMIC ACID / Delta-1-pyrroline-5-carboxylate synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLiu, J.L. / Zhong, J. / Guo, C.J. / Zhou, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2022
Title: Structural basis of dynamic P5CS filaments.
Authors: Jiale Zhong / Chen-Jun Guo / Xian Zhou / Chia-Chun Chang / Boqi Yin / Tianyi Zhang / Huan-Huan Hu / Guang-Ming Lu / Ji-Long Liu /
Abstract: The bifunctional enzyme Δ-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 ...The bifunctional enzyme Δ-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 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.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)337,3818
Polymers336,7934
Non-polymers5894
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19150 Å2
ΔGint-98 kcal/mol
Surface area112910 Å2

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate synthase


Mass: 84198.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: P5CS, Dmel\CG7470, CG7470, Dmel_CG7470
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9VNW6, glutamate 5-kinase, glutamate-5-semialdehyde dehydrogenase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
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: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
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: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 432746 / Symmetry type: POINT
RefinementCross valid method: NONE
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004920728
ELECTRON MICROSCOPYf_angle_d0.678428036
ELECTRON MICROSCOPYf_chiral_restr0.26233308
ELECTRON MICROSCOPYf_plane_restr0.00383632
ELECTRON MICROSCOPYf_dihedral_angle_d25.55022872

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