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TitleStructural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy.
Journal, issue, pagesJ Struct Biol, Vol. 205, Issue 1, Page 11-21, Year 2019
Publish dateJan 1, 2019
AuthorsHiroki Yamaguchi / Akiko Kamegawa / Kunio Nakata / Tatsuki Kashiwagi / Toshimi Mizukoshi / Yoshinori Fujiyoshi / Kazutoshi Tani /
PubMed AbstractLeucine 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 ...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.
External linksJ Struct Biol / PubMed:30543982
MethodsEM (single particle)
Resolution3.0 - 3.2 Å
Structure data

9590

6acf

EMDB-9590, PDB-6acf:
structure of leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM
Method: EM (single particle) / Resolution: 3.0 Å

9592

6ach

EMDB-9592, PDB-6ach:
Structure of NAD+-bound leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

Source
  • geobacillus stearothermophilus 10 (bacteria)
KeywordsOXIDOREDUCTASE / LEUCINE DEHYDROGENSE / NAD/LEUCINE BINDING / APO FORM / HOLO FORM

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