X-ray structure of gelonin at 1.8 Å resolution

Abstract

Gelonin is a single chain ribosome inactivating protein (RIP) with potential application in the treatment of cancer and AIDS. Diffraction quality crystals grown using PEG 3350, belong to the space group P2₁, with a=49.4 Å,b=44.9 Å,c=137.4 Å and BETA=98.4°, and contain two molecules in the asymmetric unit. Diffraction data collected to 1.8 Å resolution has a R_m value of 7.3 %. Structure of gelonin has been solved by the molecular replacement method, using ricin A chain as the search model. Crystallographic refinement using X-PLOR resulted in a model for which the r.m.s. deviations from ideal bond lengths and bond angles are 0.012 Å and 2.7°, respectively. The final R-factor is 18.4% for 39,806 reflections for which/1.0 σ(I). The C^α atoms of the two molecules in the asymmetric unit superpose to within 0.38 Å for 247 atom pairs. The overall fold of gelonin is similar to that of other RIPs such as ricin A chain and α-monorcharin, the r.m.s.d. for C^α superpositions being 1.3 and 1.4 Å, respectively. The catalytic residues (Glu166, Arg169 and Tyr113) in the active site form a hydrogen bond scheme similar to that observed in other RIPs. The conformation of Tyr74 in the active site, however, is significantly different from that in α-momorcharin. Three well defined water molecules are located in the active site cavity, and one of them, X319, superposes to within 0.2 Å of a corresponding water molecule in the structure of α-momorcharin. Any of the three could be the substrate water molecule in the hydrolysis reaction catalysed by gelonin. Difference electron density for a N-linked sugar moiety has been observed near only one of the two potential glycosylation sites in the sequence. The amino acid at position 239 has been established as Lys by calculation of omit electron density maps. The two cysteine residues in the sequence, Cys44 and Cys50, form a disulphide bond, and are therefore not available for disulphide conjugation with antibodies. Based on the structure, the region of the molecule that is involved in intradimer interactions is suggested to be suitable for introducing a Cys residue for purposes of conjugation with an antibody to produce useful immunotoxins.