Crystal structure of Malate dehydrogenase from Metallosphaera sedula

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula

Lee, D.Hong, J.Kim, K.J.

(2019) Biochem Biophys Res Commun 509: 833-838

  • DOI: https://doi.org/10.1016/j.bbrc.2019.01.018
  • Primary Citation of Related Structures:  
    6IHD, 6IHE

  • PubMed Abstract: 

    Metallosphaera sedula is a thermoacidophilic autotrophic archaeon and known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as a carbon fixation pathway. The 3-HP/4-HB cycle in M. sedula is associated with central metabolism, and malate dehydrogenase (MDH) is an enzyme involved in the central metabolism that converts malate to oxaloacetate. To elucidate the enzymatic properties of MDH from M. sedula (MsMDH), we determined the crystal structure of MsMDH as a complex with NAD + and a ternary complex with malate and NAD + . Based on its complex structures and biochemical experiments, we observed that MsMDH can utilize both NAD + and NADP + as a cofactor. In addition, we revealed that MsMDH shows a conformational change at the active site upon substrate binding. Based on the comparison with other MDHs, we revealed that MsMDH was distinguished from general MDHs due to a Lys80 residue, and this difference is likely to influence the unique cofactor specificity of MsMDH.

  • Organizational Affiliation

    School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 702-701, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase
A, B
305Metallosphaera sedulaMutation(s): 0 
Gene Names: HA72_0455
Find proteins for A0A088E2H7 (Metallosphaera sedula)
Explore A0A088E2H7 
Go to UniProtKB:  A0A088E2H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A088E2H7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.9α = 90
b = 87.9β = 90
c = 231.146γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Structure summary
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description