6ACF

structure of leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM

Summary for 6ACF

• Entry DOI: 10.2210/pdb6acf/pdb
• EMDB information: 9590
• Descriptor: Leucine dehydrogenase (1 entity in total)
• Functional Keywords: leucine dehydrogense, nad/leucine binding, apo form, oxidoreductase
• Biological source: Geobacillus stearothermophilus 10
• Total number of polymer chains: 8
• Total formula weight: 324672.16

Authors

Yamaguchi, H.,Kamegawa, A.,Nakata, K.,Kashiwagi, T.,Mizukoshi, T.,Fujiyoshi, Y.,Tani, K. (deposition date: 2018-07-26, release date: 2018-12-26, Last modification date: 2024-03-27)

Primary citation

Yamaguchi, H.,Kamegawa, A.,Nakata, K.,Kashiwagi, T.,Mizukoshi, T.,Fujiyoshi, Y.,Tani, K.
Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy
J. Struct. Biol., 205:11-21, 2019

PubMed Abstract: Leucine dehydrogenase (LDH, EC 1.4.1.9) is a NAD-dependent oxidoreductase that catalyzes the deamination of branched-chain l-amino acids (BCAAs). LDH of Geobacillus stearothermophilus (GstLDH) is a highly thermostable enzyme that has been applied for the quantification or production of BCAAs. Here the cryo-electron microscopy (cryo-EM) structures of apo and NAD-bound LDH are reported at 3.0 and 3.2 Å resolution, respectively. On comparing the structures, the two overall structures are almost identical, but it was observed that the partial conformational change was triggered by the interaction between Ser147 and the nicotinamide moiety of NAD. NAD binding also enhanced the strength of oligomerization interfaces formed by the core domains. Such additional interdomain interaction is in good agreement with our experimental results showing that the residual activity of NAD-bound form was approximately three times higher than that of the apo form after incubation at 80 °C. In addition, sequence comparison of three structurally known LDHs indicated a set of candidates for site-directed mutagenesis to improve thermostability. Subsequent mutation analysis actually revealed that non-conserved residues, including Ala94, Tyr127, and the C-terminal region, are crucial for oligomeric thermostability.

PubMed: 30543982
DOI: 10.1016/j.jsb.2018.12.001

Experimental method

ELECTRON MICROSCOPY (3 Å)