2WKF

Crystal Structure of Macrophage Migration Inhibitory Factor from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structures of macrophage migration inhibitory factor from Plasmodium falciparum and Plasmodium berghei.

Dobson, S.E.Augustijn, K.D.Brannigan, J.A.Schnick, C.Janse, C.J.Dodson, E.J.Waters, A.P.Wilkinson, A.J.

(2009) Protein Sci 18: 2578-2591

  • DOI: 10.1002/pro.263
  • Primary Citation of Related Structures:  
    2WKB, 2WKF

  • PubMed Abstract: 
  • Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses ...

    Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses. It also possesses two catalytic activities, a tautomerase and an oxidoreductase, though the physiological significance of neither reaction is known. Here, we have determined the crystal structure of MIF from two malaria parasites, Plasmodium falciparum and Plasmodium berghei at 2.2 A and 1.8 A, respectively. The structures have an alpha/beta fold and each reveals a trimer, in agreement with the results of analytical ultracentrifugation. We observed open and closed active sites, these being distinguished by movements of proline-1, the catalytic base in the tautomerase reaction. These states correlate with the covalent modification of cysteine 2 to form a mercaptoethanol adduct, an observation confirmed by mass spectrometry. The Plasmodium MIFs have a different pattern of conserved cysteine residues to the mammalian MIFs and the side chain of Cys58, which is implicated in the oxidoreductase activity, is buried. This observation and the evident redox reactivity of Cys2 suggest quite different oxidoreductase characteristics. Finally, we show in pull-down assays that Plasmodium MIF binds to the cell surface receptor CD74, a known mammalian MIF receptor implying that parasite MIF has the ability to interfere with, or modulate, host MIF activity through a competitive binding mechanism.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MACROPHAGE MIGRATION INHIBITORY FACTORA125Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1229400
EC: 5.3.2.1
UniProt
Find proteins for Q8I5C5 (Plasmodium falciparum (isolate 3D7))
Explore Q8I5C5 
Go to UniProtKB:  Q8I5C5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MACROPHAGE MIGRATION INHIBITORY FACTORB125Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1229400
EC: 5.3.2.1
UniProt
Find proteins for Q8I5C5 (Plasmodium falciparum (isolate 3D7))
Explore Q8I5C5 
Go to UniProtKB:  Q8I5C5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.253 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.291α = 90
b = 83.291β = 90
c = 83.291γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Database references, Non-polymer description
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy