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

J Biol Chem. 2021 Sep;297(3):101061. doi: 10.1016/j.jbc.2021.101061. Epub 2021 Aug 9.

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. 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.

Keywords: CD74; MIF; allosteric regulation; cytokine; tautomerase.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Site / physiology
  • Amino Acid Sequence / genetics
  • Antigens, Differentiation, B-Lymphocyte / immunology
  • Antigens, Differentiation, B-Lymphocyte / metabolism
  • Binding Sites / genetics
  • Catalytic Domain / genetics
  • Crystallography, X-Ray
  • Cytokines / immunology
  • Cytokines / metabolism
  • Histocompatibility Antigens Class II / immunology
  • Histocompatibility Antigens Class II / metabolism
  • Humans
  • Intramolecular Oxidoreductases / genetics*
  • Intramolecular Oxidoreductases / metabolism*
  • Intramolecular Oxidoreductases / physiology
  • Macrophage Migration-Inhibitory Factors / metabolism*
  • Macrophage Migration-Inhibitory Factors / physiology
  • Protein Binding / genetics
  • Structure-Activity Relationship

Substances

  • Antigens, Differentiation, B-Lymphocyte
  • Cytokines
  • Histocompatibility Antigens Class II
  • Macrophage Migration-Inhibitory Factors
  • invariant chain
  • Intramolecular Oxidoreductases
  • MIF protein, human
  • dopachrome isomerase