6ACF

structure of leucine dehydrogenase from Geobacillus stearothermophilus by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into thermostabilization of leucine dehydrogenase from its atomic structure by cryo-electron microscopy

Yamaguchi, H.Kamegawa, A.Nakata, K.Kashiwagi, T.Mizukoshi, T.Fujiyoshi, Y.Tani, K.

(2019) J Struct Biol 205: 11-21

  • DOI: 10.1016/j.jsb.2018.12.001
  • Primary Citation of Related Structures:  
    6ACH, 6ACF

  • 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 ...

    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.


    Organizational Affiliation

    Cellular and Structural Physiology Institute, Nagoya University, Chikusa, Nagoya 464-8601, Japan. Electronic address: tani@cespi.nagoya-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine dehydrogenaseA, B, C, D, E, F, G, H367Geobacillus stearothermophilus 10Mutation(s): 0 
Gene Names: GT50_15010
UniProt
Find proteins for A0A0K2HC96 (Geobacillus stearothermophilus (strain DSM 13240 / CIP 106956 / 10))
Explore A0A0K2HC96 
Go to UniProtKB:  A0A0K2HC96
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references