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- EMDB-39732: Cryo-EM structure of apo Aspergillus niger glutamate dehydrogenas... -

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Basic information

Entry
Database: EMDB / ID: EMD-39732
TitleCryo-EM structure of apo Aspergillus niger glutamate dehydrogenase (AnGDH) in the closed conformation
Map dataAnGDH closed conformation cryo-EM map
Sample
  • Complex: apo form of Aspergillus niger glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase
Keywordsglutamate dehydrogenase / allostery / cooperativity / Aspergillus / cryo-EM / domain dynamics / OXIDOREDUCTASE
Function / homology
Function and homology information


glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol
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 speciesAspergillus niger (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGodsora BKJ / Das P / Bhaumik P
Funding support India, 1 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2021/002404 India
CitationJournal: Protein Sci / Year: 2025
Title: Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase.
Authors: Barsa Kanchan Jyotshna Godsora / Parijat Das / Prasoon Kumar Mishra / Anjali Sairaman / Sandip Kaledhonkar / Narayan S Punekar / Prasenjit Bhaumik /
Abstract: Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric ...Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.
History
DepositionApr 11, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39732.png

Downloads & links

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Map

FileDownload / File: emd_39732.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnGDH closed conformation cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å		1.38 Å/pix.
x 240 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.052
Minimum - Maximum-0.19177353 - 0.36619544
Average (Standard dev.)0.00020164966 (±0.009201519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: AnGDH closed conformation half1 map

Fileemd_39732_half_map_1.map
AnnotationAnGDH closed conformation half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: AnGDH closed conformation half2 map

Fileemd_39732_half_map_2.map
AnnotationAnGDH closed conformation half2 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 : apo form of Aspergillus niger glutamate dehydrogenase

EntireName: apo form of Aspergillus niger glutamate dehydrogenase
Components
  • Complex: apo form of Aspergillus niger glutamate dehydrogenase
    • Protein or peptide: Glutamate dehydrogenase

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Supramolecule #1: apo form of Aspergillus niger glutamate dehydrogenase

SupramoleculeName: apo form of Aspergillus niger glutamate dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aspergillus niger (mold)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Glutamate dehydrogenase

MacromoleculeName: Glutamate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Aspergillus niger (mold)
Molecular weightTheoretical: 49.442508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNLPHEPEF EQAYKELAST LENSTLFQKN PEYRKALAVV SVPERVIQFR VVWEDDAGNV QVNRGFRVQF NSALGPYKGG LRFHPSVNL SILKFLGFEQ IFKNALTGLN MGGGKGGSDF DPKGKSDNEI RRFCVSFMTE LCKHIGADTD VPAGDIGVTG R EVGFLFGQ ...String:
MSNLPHEPEF EQAYKELAST LENSTLFQKN PEYRKALAVV SVPERVIQFR VVWEDDAGNV QVNRGFRVQF NSALGPYKGG LRFHPSVNL SILKFLGFEQ IFKNALTGLN MGGGKGGSDF DPKGKSDNEI RRFCVSFMTE LCKHIGADTD VPAGDIGVTG R EVGFLFGQ YRKIRNQWEG VLTGKGGSWG GSLIRPEATG YGVVYYVEHM IAHATNGQES FKGKRVAISG SGNVAQYAAL KV IELGGSV VSLSDSQGSL IINGEGSFTP EEIELIAQTK VERKQLASIV GAAPFSDANK FKYIAGARPW VHVGKVDVAL PSA TQNEIS GEEAQVLINA GCKFIAEGSN MGCTQEAIDT FEAHRTANAG AAAIWYAPGK AANAGGVAVS GLEMAQNSAR LSWT SEEVD ARLKDIMRDC FKNGLETAQE YATPAEGVLP SLVTGSNIAG FTKVAAAMKD QGDWW

UniProtKB: Glutamate dehydrogenase

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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

Concentration6 mg/mL
BufferpH: 7.5 / Details: 30 mM Phosphate buffer pH 7.5
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 27.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 2.1 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:

5xvx

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207704
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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