A family 2 pectate lyase displays a rare fold and transition metal-assisted β-elimination

The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5 angstrom, reveals it to be the first prokaryotic protein reported to display the rare (alpha/alpha)(7) barrel fold. In addition to its apo form, we have also determined the structure of a metal-bound form of YePL2A ( to 2.0 angstrom) and a trigalacturonic acid-bound substrate complex ( to 2.1 angstrom). Although its fold is rare, the catalytic center of YePL2A can be superimposed with structurally unrelated families, underlining the conserved catalytic amino acid architecture of the beta-elimination mechanism. In addition to its overall structure, YePL2A also has two other unique features: 1) it utilizes a metal atom other than calcium for catalysis, and 2) its Bronstead base is in an alternate conformation and directly interacts with the uronate group of the substrate.