3SMB

Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (MIF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural interactions dictate the kinetics of macrophage migration inhibitory factor inhibition by different cancer-preventive isothiocyanates.

Crichlow, G.V.Fan, C.Keeler, C.Hodsdon, M.Lolis, E.J.

(2012) Biochemistry 51: 7506-7514

  • DOI: 10.1021/bi3005494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulation of cellular processes by dietary nutrients is known to affect the likelihood of cancer development. One class of cancer-preventive nutrients, isothiocyanates (ITCs), derived from the consumption of cruciferous vegetables, is known to have ...

    Regulation of cellular processes by dietary nutrients is known to affect the likelihood of cancer development. One class of cancer-preventive nutrients, isothiocyanates (ITCs), derived from the consumption of cruciferous vegetables, is known to have various effects on cellular biochemistry. One target of ITCs is macrophage migration inhibitory factor (MIF), a widely expressed protein with known inflammatory, pro-tumorigenic, pro-angiogenic, and anti-apoptotic properties. MIF is covalently inhibited by a variety of ITCs, which in part may explain how they exert their cancer-preventive effects. We report the crystallographic structures of human MIF bound to phenethylisothiocyanate and to l-sulforaphane (dietary isothiocyanates derived from watercress and broccoli, respectively) and correlate structural features of these two isothiocyanates with their second-order rate constants for MIF inactivation. We also characterize changes in the MIF structure using nuclear magnetic resonance heteronuclear single-quantum coherence spectra of these complexes and observe many changes at the subunit interface. While a number of chemical shifts do not change, many of those that change do not have features similar in magnitude or direction for the two isothiocyanates. The difference in the binding modes of these two ITCs provides a means of using structure-activity relationships to reveal insights into MIF biological interactions. The results of this study provide a framework for the development of therapeutics that target MIF.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage migration inhibitory factor
A, B, C
114Homo sapiensMutation(s): 0 
Gene Names: MIF (GLIF, MMIF)
EC: 5.3.2.1
Find proteins for P14174 (Homo sapiens)
Go to Gene View: MIF
Go to UniProtKB:  P14174
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LE2
Query on LE2

Download SDF File 
Download CCD File 
A, B, C
N-(2-phenylethyl)thioformamide
Phenylethyl isothiocyanate, bound form; N-(2-phenylethyl)thiocarbamyl group
C9 H11 N S
WVJCPUDEWCGDGL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.492α = 90.00
b = 67.670β = 90.00
c = 87.771γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
AMoREphasing
CrystalCleardata collection
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description