The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms

Int J Mol Sci. 2020 Nov 7;21(21):8367. doi: 10.3390/ijms21218367.


Protein splicing catalyzed by inteins utilizes many different combinations of amino-acid types at active sites. Inteins have been classified into three classes based on their characteristic sequences. We investigated the structural basis of the protein splicing mechanism of class 3 inteins by determining crystal structures of variants of a class 3 intein from Mycobacterium chimaera and molecular dynamics simulations, which suggested that the class 3 intein utilizes a different splicing mechanism from that of class 1 and 2 inteins. The class 3 intein uses a bond cleavage strategy reminiscent of proteases but share the same Hedgehog/INTein (HINT) fold of other intein classes. Engineering of class 3 inteins from a class 1 intein indicated that a class 3 intein would unlikely evolve directly from a class 1 or 2 intein. The HINT fold appears as structural and functional solution for trans-peptidyl and trans-esterification reactions commonly exploited by diverse mechanisms using different combinations of amino-acid types for the active-site residues.

Keywords: intein; protease; protein engineering; protein evolution; protein-splicing mechanism.

MeSH terms

  • Bacterial Proteins / metabolism
  • Catalytic Domain
  • Hedgehog Proteins / genetics
  • Hedgehog Proteins / physiology*
  • Inteins / genetics
  • Inteins / physiology*
  • Molecular Dynamics Simulation
  • Mycobacterium / genetics
  • Mycobacterium / metabolism
  • Protein Splicing / genetics
  • Protein Splicing / physiology*
  • RNA Splicing / physiology


  • Bacterial Proteins
  • Hedgehog Proteins

Supplementary concepts

  • Mycobacterium chimaera