9uek | pdb_00009uek

Cryo-EM structure of L-lysine 6-dehydrogenase complex with NAD+ and L-lysine

spinqualitylabelsall models 9uek, resolution 2.53Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9uek is a 4 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 2.53Å Ligands: LYS, NAD Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function LYSDH_GEOSE Publication Abstract from PubMed l-lysine 6-dehydrogenase (LysDH; EC 1.4.1.18) oxidatively deaminates the epsilon-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 A resolution and in complex with NAD(+) and l-lysine at 2.5 A resolution. GstLysDH assembles as a tetramer, which undergoes a global conformational transition upon NAD(+) binding. Structural analysis revealed that the alpha-carboxyl and alpha-amino groups of l-lysine were coordinated by oppositely charged residues, thereby orienting the epsilon-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 epsilon-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. Structural basis for substrate recognition in l-lysine 6-dehydrogenase from Geobacillus stearothermophilus by Cryo-EM.,Funahashi T, Yamaguchi H, Suzuki S, Suzuki H, Nishikawa K, Takahashi K, Tatsumi M, Mizukoshi T, Miyano H, Fujiyoshi Y, Sugiki M J Struct Biol. 2026 Aug 28;218(4):108366. doi: 10.1016/j.jsb.2026.108366. PMID:42665198 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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