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- EMDB-64083: Cryo-EM structure of L-lysine 6-dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-64083
TitleCryo-EM structure of L-lysine 6-dehydrogenase
Map data
Sample
  • Complex: L-lysine 6-dehydrogenase
    • Protein or peptide: Lysine 6-dehydrogenase
Keywordsdehydrogenase / apo / amino acid / enzyme / OXIDOREDUCTASE
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 6-dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsFunahashi T / Yamaguchi H / Suzuki S / Suzuki H / Nishikawa K / Kazutoshi T / Fujiyoshi Y / Sugiki M
Funding support1 items
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, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64083.png

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Map

FileDownload / File: emd_64083.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 200 pix.
= 197.5 Å		0.99 Å/pix.
x 200 pix.
= 197.5 Å		0.99 Å/pix.
x 200 pix.
= 197.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9875 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.097597 - 0.15912783
Average (Standard dev.)0.000066824214 (±0.0072032027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 197.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64083_msk_1.map
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Half map: #2

Fileemd_64083_half_map_1.map
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Half map: #1

Fileemd_64083_half_map_2.map
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Sample components

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Entire : L-lysine 6-dehydrogenase

EntireName: L-lysine 6-dehydrogenase
Components
  • Complex: L-lysine 6-dehydrogenase
    • Protein or peptide: Lysine 6-dehydrogenase

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Supramolecule #1: L-lysine 6-dehydrogenase

SupramoleculeName: L-lysine 6-dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)

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Macromolecule #1: Lysine 6-dehydrogenase

MacromoleculeName: Lysine 6-dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: lysine 6-dehydrogenase
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 42.210449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKVLVLGAGL MGKEAARDLV QSQDVEAVTL ADVDLAKAEQ TVRQLHSKKL AAVRVDAGDP QQLAAAMKGH DVVVNALFYQ FNETVAKTA IETGVHSVDL GGHIGHITDR VLELHERAQA AGVTIIPDLG VAPGMINILS GYGASQLDEV ESILLYVGGI P VRPEPPLE ...String:
MKVLVLGAGL MGKEAARDLV QSQDVEAVTL ADVDLAKAEQ TVRQLHSKKL AAVRVDAGDP QQLAAAMKGH DVVVNALFYQ FNETVAKTA IETGVHSVDL GGHIGHITDR VLELHERAQA AGVTIIPDLG VAPGMINILS GYGASQLDEV ESILLYVGGI P VRPEPPLE YNHVFSLEGL LDHYTDPALI IRNGQKQEVP SLSEVEPIYF DRFGPLEAFH TSGGTSTLSR SFPNLKRLEY KT IRYRGHA EKCKLLVDLT LTRHDVEVEI NGCRVKPRDV LLSVLKPLLD LKGKDDVVLL RVIVGGRKDG KETVLEYETV TFN DRENKV TAMARTTAYT ISAVAQLIGR GVITKRGVYP PEQIVPGDVY MDEMKKRGVL ISEKRTVH

UniProtKB: Lysine 6-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

BufferpH: 10
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 761921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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