NMR structure of a KlbA intein precursor from Methanococcus jannaschii

Certain proteins of unicellular organisms are translated as precursor polypeptides containing inteins (intervening proteins), which are domains capable of performing protein splicing. These domains, in conjunction with a single residue following the intein, catalyze their own excision from the surrounding protein (extein) in a multistep reaction involving the cleavage of two intein–extein peptide bonds and the formation of a new peptide bond that ligates the two exteins to yield the mature protein. We report here the solution NMR structure of a 186‐residue precursor of the KlbA intein from Methanococcus jannaschii, comprising the intein together with N‐ and C‐extein segments of 7 and 11 residues, respectively. The intein is shown to adopt a single, well‐defined globular domain, representing a HINT (Hedgehog/Intein)‐type topology. Fourteen β‐strands are arranged in a complex fold that includes four β‐hairpins and an antiparallel β‐ribbon, and there is one α‐helix, which is packed against the β‐ribbon, and one turn of 3₁₀‐helix in the loop between the β‐strands 8 and 9. The two extein segments show increased disorder, and form only minimal nonbonding contacts with the intein domain. Structure‐based mutation experiments resulted in a proposal for functional roles of individual residues in the intein catalytic mechanism.