6ITK

Crystal structure of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase
A, B
336Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: mdhCgl2380cg2613
EC: 1.1.1.37
UniProt
Find proteins for Q8NN33 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q8NN33 
Go to UniProtKB:  Q8NN33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NN33
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.931α = 90
b = 116.94β = 95.31
c = 66.003γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

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: 2020-09-09
    Changes: Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description