Atomic resolution (1.1 Å) structure of the ribosome‐inactivating protein PD‐L4 from Phytolacca dioica L. leaves

Abstract

The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties.

Crystal structure of PD‐L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage

“…Tyr72 displays two well-defined conformations (A and B), which are similar to those observed for the atomic resolution structure of unliganded PD-L4. 35 This is consistent with the catalytic role of adenine carrier attributed to Tyr72. Indeed, as proposed earlier, the A conformation of Tyr72 likely assists RNA binding until the N-glycosidic bond has been cleaved.…”

“…In turn, Tyr72 B conformation likely stabilizes adenine in its final destination. 35 Like Tyr72, side chains of the main active site residues of PD-L1 (Tyr122, Glu175, Arg178 and Trp207) have roughly the same positioning as the corresponding residues in the structures of its homologues PD-L4 and Pokeweed Antiviral Protein (PAP).…”

“…39 In PD-L4, Asp91 is hydrogen bonded to Ser120, a residue involved in adenine binding ( Figure 7B). 35 These interactions are not conserved in the structure of PD-L1. Indeed, the entire loop is pulled back, in PD-L1 structure, due to interactions of the backbone atoms of Phe89 and Ile92 with the side chain of Arg97, a serine in PD-L4 ( Figures 7A and 7C).…”

Structure/function studies on two type 1 ribosome inactivating proteins: Bouganin and lychnin

“…Moreover, it has been proposed that in PD-L4, a type 1 RIP isolated from leaves of Phytolacca dioica, a conserved serine, the fourth residue after the catalytic tryptophan ( Fig. 1), could be also involved into the catalytic mechanism (Chambery et al, 2007;Ruggiero et al, 2008).…”

Ricin and Saporin: Plant Enzymes for the Research and the Clinics

“…pI 5.25 for Abrin A chain) [1]. Although these differences, the three-dimensional structures of these proteins are mostly super-imposable [35,[39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54] and the catalytic residues are conserved among all toxins belonging to RIPs family. In the recent years substrates other than rRNA have been identified for RIPs, with evidences that they can depurinate also DNA, mRNA and viral RNAs as well as induce nucleic acid fragmentation [55][56][57][58][59][60][61][62][63].…”