Crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro.

Lunev, S.Butzloff, S.Romero, A.R.Linzke, M.Batista, F.A.Meissner, K.A.Muller, I.B.Adawy, A.Wrenger, C.Groves, M.R.

(2018) PLoS One 13: e0195011-e0195011

  • DOI: https://doi.org/10.1371/journal.pone.0195011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Malaria remains a major threat to human health, as strains resistant to current therapeutics are discovered. Efforts in finding new drug targets are hampered by the lack of sufficiently specific tools to provide target validation prior to initiating expensive drug discovery projects. Thus, new approaches that can rapidly enable drug target validation are of significant interest. In this manuscript we present the crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH) at 2.4 Å resolution and structure-based mutagenic experiments interfering with the inter-oligomeric interactions of the enzyme. We report decreased thermal stability, significantly decreased specific activity and kinetic parameters of PfMDH mutants upon mutagenic disruption of either oligomeric interface. In contrast, stabilization of one of the interfaces resulted in increased thermal stability, increased substrate/cofactor affinity and hyperactivity of the enzyme towards malate production at sub-millimolar substrate concentrations. Furthermore, the presented data show that our designed PfMDH mutant could be used as specific inhibitor of the wild type PfMDH activity, as mutated PfMDH copies were shown to be able to self-incorporate into the native assembly upon introduction in vitro, yielding deactivated mutant:wild-type species. These data provide an insight into the role of oligomeric assembly in regulation of PfMDH activity and reveal that recombinant mutants could be used as probe tool for specific modification of the wild type PfMDH activity, thus offering the potential to validate its druggability in vivo without recourse to complex genetics or initial tool compounds. Such tool compounds often lack specificity between host or pathogen proteins (or are toxic in in vivo trials) and result in difficulties in assessing cause and effect-particularly in cases when the enzymes of interest possess close homologs within the human host. Furthermore, our oligomeric interference approach could be used in the future in order to assess druggability of other challenging human pathogen drug targets.

  • Organizational Affiliation

    Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
320Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618500
Find proteins for C6KT25 (Plasmodium falciparum (isolate 3D7))
Explore C6KT25 
Go to UniProtKB:  C6KT25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6KT25
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CIT

Download Ideal Coordinates CCD File 
AA [auth L]
BA [auth M]
CA [auth N]
DA [auth O]
EA [auth P]
AA [auth L],
BA [auth M],
CA [auth N],
DA [auth O],
EA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth H],
X [auth I],
Y [auth J],
Z [auth K]
C6 H8 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.018α = 103.77
b = 152.689β = 101.46
c = 158.393γ = 94.93
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description