7MRU

Crystal structure of S62A MIF2 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.2 of the entry. See complete history


Literature

A structurally preserved allosteric site in the MIF superfamily affects enzymatic activity and CD74 activation in D-dopachrome tautomerase.

Chen, E.Reiss, K.Shah, D.Manjula, R.Allen, B.Murphy, E.L.Murphy, J.W.Batista, V.S.Bhandari, V.Lolis, E.J.Lisi, G.P.

(2021) J Biol Chem 297: 101061-101061

  • DOI: 10.1016/j.jbc.2021.101061
  • Primary Citation of Related Structures:  
    7MRU, 7MRV, 7MSE, 7MW7

  • PubMed Abstract: 
  • The macrophage migration inhibitory factor (MIF) family of cytokines contains multiple ligand-binding sites and mediates immunomodulatory processes through an undefined mechanism(s). Previously, we reported a dynamic relay connecting the MIF catalytic site to an allosteric site at its solvent channel ...

    The macrophage migration inhibitory factor (MIF) family of cytokines contains multiple ligand-binding sites and mediates immunomodulatory processes through an undefined mechanism(s). Previously, we reported a dynamic relay connecting the MIF catalytic site to an allosteric site at its solvent channel. Despite structural and functional similarity, the MIF homolog D-dopachrome tautomerase (also called MIF-2) has low sequence identity (35%), prompting the question of whether this dynamic regulatory network is conserved. Here, we establish the structural basis of an allosteric site in MIF-2, showing with solution NMR that dynamic communication is preserved in MIF-2 despite differences in the primary sequence. X-ray crystallography and NMR detail the structural consequences of perturbing residues in this pathway, which include conformational changes surrounding the allosteric site, despite global preservation of the MIF-2 fold. Molecular simulations reveal MIF-2 to contain a comparable hydrogen bond network to that of MIF, which was previously hypothesized to influence catalytic activity by modulating the strength of allosteric coupling. Disruption of the allosteric relay by mutagenesis also attenuates MIF-2 enzymatic activity in vitro and the activation of the cluster of differentiation 74 receptor in vivo, highlighting a conserved point of control for nonoverlapping functions in the MIF superfamily.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology, & Biochemistry, Brown University, Providence, Rhode Island, USA. Electronic address: george_lisi@brown.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-dopachrome decarboxylaseA, B, C117Homo sapiensMutation(s): 1 
Gene Names: DDT
EC: 4.1.1.84
UniProt & NIH Common Fund Data Resources
Find proteins for P30046 (Homo sapiens)
Explore P30046 
Go to UniProtKB:  P30046
PHAROS:  P30046
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS (Subject of Investigation/LOI)
Query on TRS

Download Ideal Coordinates CCD File 
D [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.748α = 90
b = 75.891β = 90
c = 103.862γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2021-09-08
    Changes: Database references