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- PDB-9kl6: Crystal structure of NADP-specific glutamate dehydrogenase Gdh1 f... -

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Basic information

Entry
Database: PDB / ID: 9kl6
TitleCrystal structure of NADP-specific glutamate dehydrogenase Gdh1 from Schizosaccharomyces pombe in complex with alpha-iminoglutarate and NADP+
ComponentsNADP-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Glutamate dehydrogenase / NADP / Rossmann fold
Function / homology
Function and homology information


glutamate dehydrogenase (NADP+) / L-glutamate biosynthetic process / ammonia assimilation cycle / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / mitochondrion / nucleus / 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
(2Z)-2-iminopentanedioic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsTomita, T. / Yoshida, A. / Nishiyama, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05358 Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Phosphorylation-mediated Regulation of the NADPH-dependent Glutamate Dehydrogenase, SpGdh1, from Schizosaccharomyces pombe.
Authors: Wang, Y.F. / Tomita, T. / Yoshida, A. / Kosono, S. / Nishiyama, M.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3166
Polymers51,1471
Non-polymers1,1695
Water7,512417
1
A: NADP-specific glutamate dehydrogenase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)313,89436
Polymers306,8826
Non-polymers7,01330
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area33570 Å2
ΔGint-183 kcal/mol
Surface area81140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.965, 96.965, 188.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

21A-800-

HOH

31A-1002-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NADP-specific glutamate dehydrogenase / NADP-GDH / NADP-dependent glutamate dehydrogenase


Mass: 51146.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: gdh1, SPCC622.12c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P78804, glutamate dehydrogenase (NADP+)

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Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2IT / (2Z)-2-iminopentanedioic acid


Mass: 145.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES-NaOH, pH 7.5, 1.6M ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→46.99 Å / Num. obs: 92864 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.018 / Rrim(I) all: 0.078 / Χ2: 0.97 / Net I/σ(I): 21.5
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 99.1 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.931 / Num. measured all: 69598 / Num. unique obs: 4450 / CC1/2: 0.884 / Rpim(I) all: 0.241 / Rrim(I) all: 0.962 / Χ2: 0.94 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GUD

5gud


Resolution: 1.45→46.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.812 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20967 4666 5 %RANDOM
Rwork0.17942 ---
obs0.18095 88100 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.646 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å21.23 Å2-0 Å2
2--2.46 Å2-0 Å2
3----7.99 Å2
Refinement stepCycle: 1 / Resolution: 1.45→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 75 417 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123593
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163375
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.8184857
X-RAY DIFFRACTIONr_angle_other_deg0.6481.7567785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.963523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06110602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
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_it5.982.2041810
X-RAY DIFFRACTIONr_mcbond_other5.9782.2041810
X-RAY DIFFRACTIONr_mcangle_it7.2793.9742266
X-RAY DIFFRACTIONr_mcangle_other7.2793.9742267
X-RAY DIFFRACTIONr_scbond_it7.4192.4381783
X-RAY DIFFRACTIONr_scbond_other7.392.4351777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.8294.3882586
X-RAY DIFFRACTIONr_long_range_B_refined13.0322.534157
X-RAY DIFFRACTIONr_long_range_B_other12.08421.534050
X-RAY DIFFRACTIONr_rigid_bond_restr4.65636968
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 340 -
Rwork0.231 6329 -
obs--99.01 %

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