Azospirillum irakense pectate lyase displays a toroidal fold

The three-dimensional structure of Azospirillum irakense pectate lyase (PelA) has been determined at a resolution of 2.65 Å. The crystals are hexagonal, belonging to space group P6₅22, with unit-cell parameters a = b = 85.37, c = 231.32 Å. Phase information was derived from a multiple-wavelength anomalous dispersion (MAD) experiment using a Hg derivative. Refinement of the model converged to R_cryst = 20.08% and R_free = 25.87%. The overall structure of PelA does not adopt the characteristic parallel β-helix fold displayed by pectate lyases from polysaccharide lyase (PL) families PL1, PL3 and PL9. Instead, it displays a predominantly α-helical structure with irregular coils and short β-strands, similar to the recently reported structure of the catalytic module of the Cellvibrio japonicus pectate lyase Pel10Acm. The topologies of the two structures have been compared. They show two `domains' with the interface between them being a wide-open central groove in which the active site is located. The active sites of the crystal structures are also compared and their similarities and differences are discussed.