Lasso peptides are natural products that assume au nique lariat knot topology.L asso peptide isopeptidases (IsoPs) eliminate this topology through isopeptide bond cleavage.T op robe how these enzymes distinguish between substrates and hydrolyze only isopeptide bonds,w ee xamined the structure and mechanism of ap reviously uncharacterized IsoP from the proteobacterium Sphingopyxis alaskensis RB2256 (SpI-IsoP). We demonstrate that SpI-IsoP efficiently and specifically linearizes the lasso peptide sphingopyxin I (SpI) and variants thereof.Wealso present crystal structures of SpI and SpI-IsoP,revealing athreaded topology for the former and ap rolyl oligopeptidase (POP)-like fold for the latter. Subsequent structure-guided mutational analysis allowed us to propose roles for active-site residues.Our study sheds light on lasso peptide catabolism and expands the engineering potential of these fascinating molecules.