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- PDB-9uek: Cryo-EM structure of L-lysine 6-dehydrogenase complex with NAD+ a... -

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Basic information

Entry
Database: PDB / ID: 9uek
TitleCryo-EM structure of L-lysine 6-dehydrogenase complex with NAD+ and L-lysine
ComponentsLysine 6-dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / complex / amino acid / enzyme
Function / homology
Function and homology information


lysine 6-dehydrogenase / L-lysine 6-dehydrogenase activity / protein homooligomerization
Similarity search - Function
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
LYSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Lysine 6-dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsFunahashi, T. / Yamaguchi, H. / Suzuki, S. / Suzuki, H. / Nishikawa, K. / Kazutoshi, T. / Moemi, T. / Toshimi, M. / Hiroshi, M. / Fujiyoshi, Y. / Sugiki, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Struct Biol / Year: 2026
Title: Structural basis for substrate recognition in l-lysine 6-dehydrogenase from Geobacillus stearothermophilus by Cryo-EM.
Authors: Toshiya Funahashi / Hiroki Yamaguchi / Shota Suzuki / Hiroshi Suzuki / Kouki Nishikawa / Kazutoshi Takahashi / Moemi Tatsumi / Toshimi Mizukoshi / Hiroshi Miyano / Yoshinori Fujiyoshi / Masayuki Sugiki /
Abstract: l-lysine 6-dehydrogenase (LysDH; EC 1.4.1.18) oxidatively deaminates the ε-amino group of l-lysine. Due to its high substrate specificity, LysDH serves as a valuable tool for l-lysine quantification. ...l-lysine 6-dehydrogenase (LysDH; EC 1.4.1.18) oxidatively deaminates the ε-amino group of l-lysine. Due to its high substrate specificity, LysDH serves as a valuable tool for l-lysine quantification. However, the molecular basis of this specificity has remained unclear because of the lack of substrate-bound structures. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of LysDH from the thermophilic bacterium Geobacillus stearothermophilus (GstLysDH) in the apo form at 2.9 Å resolution and in complex with NAD and l-lysine at 2.5 Å resolution. GstLysDH assembles as a tetramer, which undergoes a global conformational transition upon NAD binding. Structural analysis revealed that the α-carboxyl and α-amino groups of l-lysine were coordinated by oppositely charged residues, thereby orienting the ε-amino group toward the nicotinamide ring of NAD and anchoring the substrate in the optimal binding mode. This precise recognition mechanism accounts for the enzyme's strict specificity for the ε-amino group of l-lysine. Furthermore, comparative structural analysis with l-phenylalanine dehydrogenase suggests that the oxidative deamination in GstLysDH proceeds through a conserved hydride transfer mechanism. Together, these insights establish a structural framework for the rational design and industrial application of LysDH and related amino acid dehydrogenases.
History
DepositionApr 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine 6-dehydrogenase
B: Lysine 6-dehydrogenase
C: Lysine 6-dehydrogenase
D: Lysine 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,08412
Polymers168,8424
Non-polymers3,2428
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 384 / Label seq-ID: 1 - 384

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lysine 6-dehydrogenase / L-lysine 6-dehydrogenase / L-lysine epsilon-dehydrogenase


Mass: 42210.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: lysDH / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AJC6, lysine 6-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: L-lysine 6-dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 10
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2REFMAC5.8.0267model refinement
13RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 672092 / Symmetry type: POINT
RefinementResolution: 2.53→2.53 Å / Cor.coef. Fo:Fc: 0.881 / SU B: 11.391 / SU ML: 0.225 / ESU R: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33752 --
obs0.33752 230362 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 61.859 Å2
Refinement stepCycle: 1 / Total: 12108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01312280
ELECTRON MICROSCOPYr_bond_other_d0.0330.01512052
ELECTRON MICROSCOPYr_angle_refined_deg1.2071.64716664
ELECTRON MICROSCOPYr_angle_other_deg1.451.58227752
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.48551532
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.56421.788604
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.014152168
ELECTRON MICROSCOPYr_dihedral_angle_4_deg24.1991592
ELECTRON MICROSCOPYr_chiral_restr0.0640.21624
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0213696
ELECTRON MICROSCOPYr_gen_planes_other0.0090.022580
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.366.1466152
ELECTRON MICROSCOPYr_mcbond_other3.366.1476151
ELECTRON MICROSCOPYr_mcangle_it5.5939.2357676
ELECTRON MICROSCOPYr_mcangle_other5.5939.2347677
ELECTRON MICROSCOPYr_scbond_it5.4166.9796128
ELECTRON MICROSCOPYr_scbond_other5.4166.9796128
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.41510.1028988
ELECTRON MICROSCOPYr_long_range_B_refined13.13773.50812856
ELECTRON MICROSCOPYr_long_range_B_other13.13673.50712857
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A233100.15
12B233100.15
21A230440.16
22C230440.16
31A232260.15
32D232260.15
41B228740.16
42C228740.16
51B229540.16
52D229540.16
61C231800.16
62D231800.16
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.142 17079 -
obs--100 %

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