The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin

Demonstration of ribonuclease activity in the plant ribosome-inactivating proteins alpha- and beta-momorcharins

Alpha- and beta-momorcharins, ribosome-inactivating proteins from Momordica charantia seeds, were utilized in this investigation. Ribonucleolytic cleavage was observed after naked rRNA was incubated with either momorcharin. Beta-momorcharin, and to a lesser extent alpha-momorcharin, also acted on tRNA to release acid-soluble UV-absorbing products. Such activity was optimal at pH around 5.5. Using polyhomoribonucleotides as substrate, it was found that the momorcharins preferentially acted on polyU, but exerted negligible effects on polyA, polyC and polyG. Chromatographic analysis of the reaction product indicated that mono and/or oligo-ribonucleotides, but not free base, were generated from polyU, suggesting that the enzymatic action involved ribonucleolytic cleavage. Similar to the results obtained with tRNA as substrate, beta-momorcharin was about 15-fold more active than alpha-momorcharin on polyU.

Modeling of the three-dimensional structure of luffin-alpha and its simulated reaction with the substrate oligoribonucleotide GAGA

A fundamental problem in biochemistry and molecular biology is understanding the spatial structure of macromolecules and then analyzing their functions. In this study, the three-dimensional structure of a ribosome-inactivating protein luffin-alpha was predicted using a neural network method and molecular dynamics simulation. A feedforward neural network with the backpropagation learning algorithm were trained on model class of homologous proteins including trichosanthin and alpha-momorcharin. The distance constraints for the C alpha atoms in the protein backbone were utilized to generate a folded crude conformation of luffin-alpha by model building and the steepest descent minimization approach. The crude conformation was refined by molecular dynamics techniques and a simulated annealing procedure. The interaction between luffin-alpha and its analogous substrate GAGA was also simulated to understand its action mechanism.

High-resolution NMR study of a GdAGA tetranucleotide loop that is an improved substrate for ricin, a cytotoxic plant protein

Ricin is a cytotoxic plant protein that inactivates ribosomes by hydrolyzing the N-glycosidic bond at position A4324 in eukaryotic 28S rRNA. Recent studies showed that a four-nucleotide loop, GAGA, can function as a minimum substrate for ricin (the first adenosine corresponds to the site of depurination). We previously clarified the solution structure of this loop by NMR spectroscopy [Orita et al. (1993) Nucleic Acids Res. 21, 5670-5678]. To elucidate further details of the structural basis for recognition of its substrate by ricin, we studied the properties of a synthetic dodecanucleotide, r1C2U3C4A5G6dA7G8A9U10G11A12G (6dA12mer), which forms an RNA hairpin structure with a GdAGA loop and in which the site of depurination is changed from adenosine to 2'-deoxyadenosine. The N-glycosidase activity against the GdAGA loop of the A-chain of ricin was 26 times higher than that against the GAGA loop. NMR studies indicated that the overall structure of the GdAGA loop was similar to that of the GAGA loop with the exception of the sugar puckers of 6dA and 7G. Therefore, it appears that the 2'-hydroxyl group of adenosine at the depurination site (6A) does not participate in the recognition by ricin of the substrate. Since the 2'-hydroxyl group can potentially destabilize the developing positive charge of the putative transition state intermediate, an oxycarbonium ion, the electronic effect may explain, at least in part, the faster rate of depurination of the GdAGA loop compared to that of GAGA loop. We also show that the amino group of 7G is essential for substrate recognition the ricin A-chain.

Crystallization and preliminary crystallographic analysis of recombinant abrin-a A-chain with ribosome inactivating activity

Crystals have been obtained for a recombinant abrin-a A-chain produced by E. coli. The crystals were grown using PEG6000 as the precipitating agent. The crystals belong to an orthrhombic space group (P2(1)2(1)2(1)) and diffract to 1.7 A.

Identification of a stable complex of trichosanthin with nicotinamide adenine dinucleotide phosphate

Trichosanthin, a type I ribosome-inactivating protein with RNA N-glycosidase activity, forms a stable complex with nicotinamide adenine dinucleotide phosphate, a substrate analog. Difference UV spectroscopy, fluorescence spectroscopy, and 31P NMR are used to identify the formation of the complex, followed by a crystal structure analysis carried out to elucidate the active-site structure of trichosanthin. The determination of germinal vesicle breakdown indicates that the complex does not, at least for abortion-inducing activity, result in competitive inhibition to the protein.

Crystal structure of trichosanthin-NADPH complex at 1.7 A resolution reveals active-site architecture

We describe here the crystal structure of the trichosanthin-NADPH complex determined at a resolution of 1.7 A. The adenine base stacks between Tyr 70 and Tyr 111. Arg 163, Glu 160 and Tyr 70 form hydrogen bonds to N(3), O(3') and, through a water molecule, to N(9) of adenosine, respectively. This is the first high resolution structure of a complex between a ribosome-inactivating protein and a substrate analogue, in which the electron density of the N-glycosidic bond is well defined and the preassociated water, thought to be responsible for hydrolyzing the N-C bond, is also explicitly elucidated.