1MFI

CRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR COMPLEXED WITH (E)-2-FLUORO-P-HYDROXYCINNAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of macrophage migration inhibitory factor complexed with (E)-2-fluoro-p-hydroxycinnamate at 1.8 A resolution: implications for enzymatic catalysis and inhibition.

Taylor, A.B.Johnson Jr., W.H.Czerwinski, R.M.Li, H.S.Hackert, M.L.Whitman, C.P.

(1999) Biochemistry 38: 7444-7452

  • DOI: 10.1021/bi9904048
  • Primary Citation of Related Structures:  
    1MFI

  • PubMed Abstract: 
  • Macrophage migration inhibitory factor (MIF) exhibits dual activities. It acts as an immunoregulatory protein as well as a phenylpyruvate tautomerase. To understand better the relationship between these two activities and to elucidate the structural basis for the enzymatic activity, a crystal structure of a complex between murine MIF and (E)-2-fluoro-p-hydroxycinnamate, a competitive inhibitor of the tautomerase activity, has been determined to 1 ...

    Macrophage migration inhibitory factor (MIF) exhibits dual activities. It acts as an immunoregulatory protein as well as a phenylpyruvate tautomerase. To understand better the relationship between these two activities and to elucidate the structural basis for the enzymatic activity, a crystal structure of a complex between murine MIF and (E)-2-fluoro-p-hydroxycinnamate, a competitive inhibitor of the tautomerase activity, has been determined to 1.8 A resolution. The structure is nearly superimposable on that of the free protein indicating that the presence of the inhibitor does not result in any major structural changes. The inhibitor also confirms the location of the active site in a hydrophobic cavity containing the amino-terminal proline. Within this cavity, the inhibitor interacts with residues from adjacent subunits. At the back of the cavity, the side-chain carbonyl oxygen of Asn-97' interacts with the phenolic hydroxyl group of the inhibitor while at the mouth of the cavity the ammonium group of Lys-32 interacts with a carboxylate oxygen. The other carboxylate oxygen of the inhibitor interacts with Pro-1. The hydroxyl group of Tyr-95' interacts weakly with the fluoro group on the inhibitor. The hydrophobic side chains of five active-site residues (Met-2, Ile-64, Met-101, Val-106, and Phe-113) and the phenyl moiety of Tyr-95' are responsible for the binding of the phenyl group. Further insight into the enzymatic activity of MIF was obtained by carrying out kinetic studies using the enol isomers of phenylpyruvate and (p-hydroxyphenyl)pyruvate. The results demonstrate that MIF processes the enol isomers more efficiently than the keto isomers primarily because of a decrease in Km. On the basis of these results, a mechanism is proposed for the MIF-catalyzed tautomerization reaction.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Medicinal Chemistry Division, College of Pharmacy, The University of Texas, Austin 78712-1071, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (MACROPHAGE MIGRATION INHIBITORY FACTOR)A, B, C114Mus musculusMutation(s): 0 
Gene Names: Mif
EC: 5.3.2.1 (UniProt), 5.3.3.12 (UniProt)
UniProt
Find proteins for P34884 (Mus musculus)
Explore P34884 
Go to UniProtKB:  P34884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34884
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FHC
Query on FHC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE
C9 H6 F O3
SBIZDOWXYPNTOJ-VMPITWQZSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FHC Binding MOAD:  1MFI Ki: 2600 (nM) from 1 assay(s)
PDBBind:  1MFI Ki: 2600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.53α = 90
b = 99.53β = 90
c = 105.69γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection