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- EMDB-35901: GK tetramer with adjacent hooks at reaction state -

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Basic information

Entry
Database: EMDB / ID: EMD-35901
TitleGK tetramer with adjacent hooks at reaction state
Map data
Sample
  • Complex: Arabidopsis thaliana P5CSB incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsL-proline biosynthesis / filamentous enzyme / PLANT PROTEIN
Function / homology
Function and homology information


glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / L-proline biosynthetic process / embryo development ending in seed dormancy / proline biosynthetic process / plasmodesma / chloroplast ...glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / L-proline biosynthetic process / embryo development ending in seed dormancy / proline biosynthetic process / plasmodesma / chloroplast / ATP binding / cytoplasm
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 B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang T / Guo CJ / Liu JL
Funding support China, 1 items
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
DepositionApr 10, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35901.png

Downloads & links

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Map

FileDownload / File: emd_35901.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.009686425 - 0.022491764
Average (Standard dev.)0.00007136869 (±0.0009389028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35901_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35901_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana P5CSB incubated with all substrates.

EntireName: Arabidopsis thaliana P5CSB incubated with all substrates.
Components
  • Complex: Arabidopsis thaliana P5CSB incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: GAMMA-GLUTAMYL PHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Arabidopsis thaliana P5CSB incubated with all substrates.

SupramoleculeName: Arabidopsis thaliana P5CSB incubated with all substrates.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.9 kDa/nm

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

MacromoleculeName: Delta-1-pyrroline-5-carboxylate synthase B / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.97732 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTEIDRSRAF AKDVKRIVVK VGTAVVTGKG GRLALGRLGA ICEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSSF ADLQKPQME LDGKACAGVG QSSLMAYYET MFDQLDVTVA QMLVTDSSFR DKDFRKQLSE TVKAMLRMRV IPVFNENDAI S TRRAPYKD ...String:
MTEIDRSRAF AKDVKRIVVK VGTAVVTGKG GRLALGRLGA ICEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSSF ADLQKPQME LDGKACAGVG QSSLMAYYET MFDQLDVTVA QMLVTDSSFR DKDFRKQLSE TVKAMLRMRV IPVFNENDAI S TRRAPYKD STGIFWDNDS LAALLSLELK ADLLILLSDV EGLYTGPPSD STSKLIHTFI KEKHQDEITF GEKSKLGRGG MT AKVKAAV NAAYGGVPVI ITSGYAAENI SKVLRGLRVG TLFHQDAHLW APVVDTTSRD MAVAARESSR KLQALSSEDR KQI LHDIAN ALEVNEKTIK AENDLDVAAA QEAGYEESLV ARLVMKPGKI SSLAASVRQL AEMEDPIGRV LKKTQVADDL ILEK TSSPI GVLLIVFESR PDALVQIASL AIRSGNGLLL KGGKEARRSN AILHKVITDA IPETVGGKLI GLVTSREEIP DLLKL DDVI DLVIPRGSNK LVSQIKNSTK IPVLGHADGI CHVYVDKSGK LDMAKRIVSD AKLDYPAACN AMETLLVHKD LEQNGF LDD LIYVLQTKGV TLYGGPRASA KLNIPETKSF HHEYSSKACT VEIVEDVYGA IDHIHQHGSA HTDCIVTEDS EVAEIFL RQ VDSAAVFHNA STRFSDGFRF GLGAEVGIST SRIHARGPVG VEGLLTTRWI MRGKGQVVDG DNGIVYTHKD LPVLQRTE A VENGI

UniProtKB: Delta-1-pyrroline-5-carboxylate synthase B

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / 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 #3: GAMMA-GLUTAMYL PHOSPHATE

MacromoleculeName: GAMMA-GLUTAMYL PHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: RGP
Molecular weightTheoretical: 227.109 Da
Chemical component information

ChemComp-RGP:
GAMMA-GLUTAMYL PHOSPHATE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wx3

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223041
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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