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TitleStructural basis for substrate recognition in l-lysine 6-dehydrogenase from Geobacillus stearothermophilus by Cryo-EM.
Journal, issue, pagesJ Struct Biol, Vol. 218, Issue 4, Page 108366, Year 2026
Publish dateAug 28, 2026
AuthorsToshiya Funahashi / Hiroki Yamaguchi / Shota Suzuki / Hiroshi Suzuki / Kouki Nishikawa / Kazutoshi Takahashi / Moemi Tatsumi / Toshimi Mizukoshi / Hiroshi Miyano / Yoshinori Fujiyoshi / Masayuki Sugiki /
PubMed Abstractl-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.
External linksJ Struct Biol / PubMed:42665198
MethodsEM (single particle)
Resolution2.53 - 2.94 Å
Structure data

64083

9uej

EMDB-64083, PDB-9uej:
Cryo-EM structure of L-lysine 6-dehydrogenase
Method: EM (single particle) / Resolution: 2.94 Å

64084

9uek

EMDB-64084, PDB-9uek:
Cryo-EM structure of L-lysine 6-dehydrogenase complex with NAD+ and L-lysine
Method: EM (single particle) / Resolution: 2.53 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-LYS:
LYSINE

ChemComp-HOH:
WATER

Source
  • geobacillus stearothermophilus (bacteria)
KeywordsOXIDOREDUCTASE / dehydrogenase / apo / amino acid / enzyme / complex

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