Malate Dehydrogenase from Geobacillus stearothermophilus (gs-MDH) G218Y mutant

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.179 

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Increasing loop flexibility affords low-temperature adaptation of a moderate thermophilic malate dehydrogenase from Geobacillus stearothermophilus.

Shimozawa, Y.Himiyama, T.Nakamura, T.Nishiya, Y.

(2021) Protein Eng Des Sel 34

  • DOI: https://doi.org/10.1093/protein/gzab026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Malate dehydrogenase (MDH) catalyzes the reversible reduction of nicotinamide adenine dinucleotide from oxaloacetate to L-malate. MDH from moderate thermophilic Geobacillus stearothermophilus (gs-MDH) has high thermal stability and substrate specificity and is used as a diagnostic reagent. In this study, gs-MDH was engineered to increase its catalytic activity at low temperatures. Based on sequential and structural comparison with lactate dehydrogenase from G. stearothermophilus, we selected G218 as a mutation site to increase the loop flexibility pivotal for MDH catalysis. The G218 mutants showed significantly higher specific activities than the wild type at low temperatures and maintained thermal stability. The crystal structure of the G218Y mutant, which had the highest catalytic efficiency among all the G218 mutants, suggested that the flexibility of the mobile loop was successfully increased by the bulky side chain. Therefore, this study demonstrated the low-temperature adaptation of MDH by facilitating conformational changes during catalysis.

  • Organizational Affiliation

    Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka 572-8508, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase
A, B, C, D
332Geobacillus stearothermophilusMutation(s): 1 
Gene Names: mdh
Find proteins for A0A143T1U9 (Geobacillus stearothermophilus)
Explore A0A143T1U9 
Go to UniProtKB:  A0A143T1U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A143T1U9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.424α = 90
b = 110.22β = 90
c = 150.827γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06616
Japan Society for the Promotion of Science (JSPS)Japan20K15403
Japan Society for the Promotion of Science (JSPS)Japan20K05740

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description