Structure of Macrophage Migration Inhibitory Factor Covalently Inhibited by PMSF Treatment

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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This is version 1.3 of the entry. See complete history


Structural and kinetic analyses of macrophage migration inhibitory factor active site interactions.

Crichlow, G.V.Lubetsky, J.B.Leng, L.Bucala, R.Lolis, E.J.

(2009) Biochemistry 48: 132-139

  • DOI: https://doi.org/10.1021/bi8014423
  • Primary Citation of Related Structures:  
    3CE4, 3DJH, 3DJI

  • PubMed Abstract: 

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  • Organizational Affiliation

    Department of Pharmacology and Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens)
Explore P14174 
Go to UniProtKB:  P14174
PHAROS:  P14174
GTEx:  ENSG00000240972 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14174
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PMS

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
N [auth C]
phenylmethanesulfonic acid
C7 H8 O3 S
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
L [auth C],
M [auth C]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
O [auth C]
C3 H8 O3
Query on IPA

Download Ideal Coordinates CCD File 
K [auth B],
P [auth C]
C3 H8 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.403α = 90
b = 67.505β = 90
c = 88.826γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
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: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description