9uej: Difference between revisions
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==Cryo-EM structure of L-lysine 6-dehydrogenase== | |||
<StructureSection load='9uej' size='340' side='right'caption='[[9uej]], [[Resolution|resolution]] 2.94Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9uej]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9UEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9UEJ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.94Å</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9uej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9uej OCA], [https://pdbe.org/9uej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9uej RCSB], [https://www.ebi.ac.uk/pdbsum/9uej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9uej ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/LYSDH_GEOSE LYSDH_GEOSE] | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:42665198</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9uej" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Geobacillus stearothermophilus]] | |||
[[Category: Large Structures]] | |||
[[Category: Fujiyoshi Y]] | |||
[[Category: Funahashi T]] | |||
[[Category: Kazutoshi T]] | |||
[[Category: Nishikawa K]] | |||
[[Category: Sugiki M]] | |||
[[Category: Suzuki H]] | |||
[[Category: Suzuki S]] | |||
[[Category: Yamaguchi H]] | |||
