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- PDB-8z2c: Crystal structure of apo Aspergillus terreus glutamate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 8z2c
TitleCrystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I)
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase / allostery / cooperativity / Aspergillus / domain dynamics
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
ACETATE ION / Glutamate dehydrogenase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGodsora, B.K.J. / Bhaumik, P.
Funding support India, 1items
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 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glutamate dehydrogenase
A: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7316
Polymers98,4952
Non-polymers2364
Water5,332296
1
B: Glutamate dehydrogenase
A: Glutamate dehydrogenase
hetero molecules

B: Glutamate dehydrogenase
A: Glutamate dehydrogenase
hetero molecules

B: Glutamate dehydrogenase
A: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,19318
Polymers295,4856
Non-polymers70912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area25840 Å2
ΔGint-12 kcal/mol
Surface area88610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.120, 156.120, 106.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Glutamate dehydrogenase


Mass: 49247.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: gdhA, ATETN484_0007063400 / Production host: Escherichia coli (E. coli) / References: UniProt: T2D1F5
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 95195 / % possible obs: 98.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 26.24 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.9
Reflection shellResolution: 2.05→2.15 Å / Num. unique obs: 11999 / CC1/2: 0.58 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ECS

7ecs


Resolution: 2.05→29.77 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.265 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 4670 5.1 %RANDOM
Rwork0.17601 ---
obs0.1774 87330 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.029 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2--1.94 Å20 Å2
3----3.88 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 16 296 7220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137414
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156994
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.63210088
X-RAY DIFFRACTIONr_angle_other_deg1.4341.58116108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2695993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89822.722360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.804151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3541542
X-RAY DIFFRACTIONr_chiral_restr0.0920.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028824
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021748
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9572.8653874
X-RAY DIFFRACTIONr_mcbond_other2.9572.8643871
X-RAY DIFFRACTIONr_mcangle_it3.7274.294897
X-RAY DIFFRACTIONr_mcangle_other3.7274.294898
X-RAY DIFFRACTIONr_scbond_it3.3143.0683540
X-RAY DIFFRACTIONr_scbond_other3.3143.0693541
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4254.535192
X-RAY DIFFRACTIONr_long_range_B_refined5.70434.5058595
X-RAY DIFFRACTIONr_long_range_B_other5.68634.4888568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 345 -
Rwork0.276 6383 -
obs--99.81 %

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