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- EMDB-32875: GK domain of Drosophila P5CS filament with glutamate, ATP, and NADPH -

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Basic information

Entry
Database: EMDB / ID: EMD-32875
TitleGK domain of Drosophila P5CS filament with glutamate, ATP, and NADPH
Map data
Sample
  • Organelle or cellular component: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
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
Delta-1-pyrroline-5-carboxylate synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu JL / Zhong J / Guo CJ / Zhou X
Funding support China, 1 items
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
DepositionFeb 14, 2022-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 6, 2022-
Current statusApr 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32875.png

Downloads & links

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Map

FileDownload / File: emd_32875.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.17639337 - 0.33054745
Average (Standard dev.)4.8982158e-05 (±0.006098122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32875_msk_1.map
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Half map: #1

Fileemd_32875_half_map_1.map
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Half map: #2

Fileemd_32875_half_map_2.map
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Sample components

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Entire : Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase

EntireName: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase
Components
  • Organelle or cellular component: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase

SupramoleculeName: Drosophila glutamate-bound Delta-1-pyrroline-5-carboxylate synthase
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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

MacromoleculeName: Delta-1-pyrroline-5-carboxylate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 84.198227 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MLQNSFKLAQ SLRNGFYRNA WRAFSSHGPR QPLVSPERRL EKAHPTFTER SQLKYARRLV VKLGSAVITR EDNHGLALGR LASIVEQVA ECHLEGREVM MVTSGAVAFG KQKLAQELLM SLSMRETLNP KDSKEFDGAT LEPRAAAAVG QSGLMSLYDA M FAQYGVKI ...String:
MLQNSFKLAQ SLRNGFYRNA WRAFSSHGPR QPLVSPERRL EKAHPTFTER SQLKYARRLV VKLGSAVITR EDNHGLALGR LASIVEQVA ECHLEGREVM MVTSGAVAFG KQKLAQELLM SLSMRETLNP KDSKEFDGAT LEPRAAAAVG QSGLMSLYDA M FAQYGVKI AQVLVTKPDF YNEETRNNLF CTLSELISLN IVPIINTNDA VSPPMFIRDD EPAGGARRGI PIKDNDSLSA ML AAEVQAD LLILMSDVDG IYNKPPWEDG AKLMHTYTSD DSNSIEFGKK SKVGTGGMDS KVKAATWALD RGVSVVICNG MQE KAIKTI IGGRKVGTFF TEATESANAV PVEVMAENAR TGSRQMQALT PAQRASAVNT LADLLVSREK FILDANAKDL AEAQ KSGLA KPLLSRLSLN PAKLKNLSVG LKQIAEDSHK NVGRVLRRTR LADQLELKQV TVPIGVLLVI FESRPDSLPQ VAALA MASA NGLLLKGGKE AAHSNKALME LVKEALATVG AEHAVSLVST REEISDLLSM ENHIDLIIPR GSSDLVRSIQ QQSLHI PVL GHAEGVCHVY IDRDADLEKA LRIARDAKCD YPAACNAMET LLIHEDLMSG AIFGDVCNML KREGVKIYAG PRLNQQL TF GPPAAKSLKH EYGALECCIE VVPSLDEAIN HIHTYGSSHT DVIVTENDAA ARQFLGSVDS ACVFHNASSR FADGFRFG L GAEVGISTAR IHARGPVGVE GLLTTKWILE GQDHAAADFA EGGGRTWLHE TLPLD

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Macromolecule #2: GAMMA-GLUTAMYL PHOSPHATE

MacromoleculeName: GAMMA-GLUTAMYL PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: RGP
Molecular weightTheoretical: 227.109 Da
Chemical component information

ChemComp-RGP:
GAMMA-GLUTAMYL PHOSPHATE

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1412498
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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