Crystal structure of malate dehydrogenase from Mannheimia succiniciproducens in complex with NAD

Experimental Data Snapshot

  • Resolution: 1.97 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase.

Ahn, J.H.Seo, H.Park, W.Seok, J.Lee, J.A.Kim, W.J.Kim, G.B.Kim, K.J.Lee, S.Y.

(2020) Nat Commun 11: 1970-1970

  • DOI: https://doi.org/10.1038/s41467-020-15839-z
  • Primary Citation of Related Structures:  
    6ITK, 6ITL

  • PubMed Abstract: 

    Succinic acid (SA), a dicarboxylic acid of industrial importance, can be efficiently produced by metabolically engineered Mannheimia succiniciproducens. Malate dehydrogenase (MDH) is one of the key enzymes for SA production, but has not been well characterized. Here we report biochemical and structural analyses of various MDHs and development of hyper-SA producing M. succiniciproducens by introducing the best MDH. Corynebacterium glutamicum MDH (CgMDH) shows the highest specific activity and least substrate inhibition, whereas M. succiniciproducens MDH (MsMDH) shows low specific activity at physiological pH and strong uncompetitive inhibition toward oxaloacetate (ki of 67.4 and 588.9 μM for MsMDH and CgMDH, respectively). Structural comparison of the two MDHs reveals a key residue influencing the specific activity and susceptibility to substrate inhibition. A high-inoculum fed-batch fermentation of the final strain expressing cgmdh produces 134.25 g L -1 of SA with the maximum productivity of 21.3 g L -1  h -1 , demonstrating the importance of enzyme optimization in strain development.

  • Organizational Affiliation

    Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase320[Mannheimia] succiniciproducens MBEL55EMutation(s): 0 
Gene Names: mdhMS1266
Find proteins for Q65T37 (Mannheimia succiniciproducens (strain MBEL55E))
Explore Q65T37 
Go to UniProtKB:  Q65T37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65T37
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C21 H27 N7 O14 P2
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.97 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.089α = 90
b = 80.089β = 90
c = 193.15γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-09-16
    Changes: Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description