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- EMDB-60270: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Th... -

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Basic information

Entry
Database: EMDB / ID: EMD-60270
TitleCryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus in complex with NADPH and AKG in the steady stage of reaction
Map data
Sample
  • Complex: Hexamer of W89F mutated glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: water
KeywordsOxidoreductase / Complex / NADPH / 2-oxoglutarate / Mutant
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process
Similarity search - Function
: / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...: / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutamate dehydrogenase
Similarity search - Component
Biological speciesThermococcus profundus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWakabayashi T / Nakasako M
Funding support Japan, 13 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)jp13480214 Japan
Japan Society for the Promotion of Science (JSPS)jp19204042 Japan
Japan Society for the Promotion of Science (JSPS)jp22244054 Japan
Japan Society for the Promotion of Science (JSPS)jp21H01050 Japan
Japan Society for the Promotion of Science (JSPS)jp26800227 Japan
Japan Society for the Promotion of Science (JSPS)18J11653 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp15076210 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp20050030 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp22018027 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp23120525 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp25120725 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp15H01647 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)jp17H05891 Japan
CitationJournal: To Be Published
Title: Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by crystal structure and cryoEM-sampling of metastable conformation in action
Authors: Wakabayashi T / Oide M / Matsui Y / Nakasako M
History
DepositionMay 26, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60270.png

Downloads & links

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Map

FileDownload / File: emd_60270.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.024142569 - 0.044467572
Average (Standard dev.)0.000053420747 (±0.002058596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 192.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60270_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_60270_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 : Hexamer of W89F mutated glutamate dehydrogenase

EntireName: Hexamer of W89F mutated glutamate dehydrogenase
Components
  • Complex: Hexamer of W89F mutated glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 2-OXOGLUTARIC ACID
  • Ligand: water

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Supramolecule #1: Hexamer of W89F mutated glutamate dehydrogenase

SupramoleculeName: Hexamer of W89F mutated glutamate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermococcus profundus (archaea)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Glutamate dehydrogenase

MacromoleculeName: Glutamate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutamate dehydrogenase [NAD(P)+]
Source (natural)Organism: Thermococcus profundus (archaea)
Molecular weightTheoretical: 46.360004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IDPFEMAVKQ LERAAQYMDI SEEALEWLKK PMRIVEVSVP IEMDDGSVKV FTGFRVQHNW ARGPTKGGIR WHPAETLSTV KALATFMTW KVAVVDLPYG GGKGGIIVNP KELSEREQER LARAYIRAVY DVIGPWTDIP APDVYTNPKI MGWMMDEYET I MRRKGPAF ...String:
IDPFEMAVKQ LERAAQYMDI SEEALEWLKK PMRIVEVSVP IEMDDGSVKV FTGFRVQHNW ARGPTKGGIR WHPAETLSTV KALATFMTW KVAVVDLPYG GGKGGIIVNP KELSEREQER LARAYIRAVY DVIGPWTDIP APDVYTNPKI MGWMMDEYET I MRRKGPAF GVITGKPLSI GGSLGRGTAT AQGAIFTIRE AAKALGIDLK GKKIAVQGYG NAGYYTAKLA KEQLGMTVVA VS DSRGGIY NPDGLDPDEV LKWKREHGSV KDFPGATNIT NEELLELEVD VLAPAAIEEV ITEKNADNIK AKIVAEVANG PVT PEADDI LREKGILQIP DFLCNAGGVT VSYFEWVQNI NGYYWTEEEV REKLDKKMTK AFWEVYNTHK DKNIHMRDAA YVVA VSRVY QAMKDRGWVK K

UniProtKB: Glutamate dehydrogenase

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Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 2 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: 2-OXOGLUTARIC ACID

MacromoleculeName: 2-OXOGLUTARIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: AKG
Molecular weightTheoretical: 146.098 Da
Chemical component information

ChemComp-AKG:
2-OXOGLUTARIC ACID

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 16 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration9.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.5 mMC21H27N7NaO17P3Sodium Nicotiamide adenine dinucleotide phosphate
100.0 mMC5H8NNaO4monosodium glutamate
5.0 mMC4H11NO3tris(hydroxymethyl)aminomethane

Details: 0.5 mM NADP, 100 mM Glutamate in 5 mM Tris-HCl at pH7.5.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: The sample solution was flash-frozen 2-h after mixing the protein solution and buffer solution..
Details8.96 mg/mL GDH W89F

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7651 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.35000000000000003 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3534400
Startup modelType of model: INSILICO MODEL
Details: The startup model was generated by de novo 3D model generation in Relion.
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 232476
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 32 / Avg.num./class: 115000 / Software - Name: RELION (ver. 4.0)
Details: The final 3D classification carried out by two-step process. In the first, all particles were separated into eight classes. Subsequently, each of these classes was further classified into ...Details: The final 3D classification carried out by two-step process. In the first, all particles were separated into eight classes. Subsequently, each of these classes was further classified into four subclasses. This entire process was conducted following a symmetry expansion operation on all particles, in accordance with the D3 symmetry of GDH.
FSC plot (resolution estimation)

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