Pokeweed antiviral protein inactivates pokeweed ribosomes; implications for the antiviral mechanism

Pokeweed antiviral protein (PAP) and other ribosome-inactivating proteins (RIPs) had previously been thought to be incapable of attacking conspecific ribosomes, thus having no effect on endogenous processes. This assertion conflicts with a model for PAP's in vivo antiviral mechanism in which PAP (a cell wall protein) selectively enters virus-infected cells and disrupts protein synthesis, thus causing local suicide and preventing virus replication. We show here that pokeweed (Phytolacca americana) ribosomes, as well as endod (Phytolacca dodecandra) ribosomes, are indeed highly sensitive to inactivation by conspecific RIPs. Ribosomes isolated from RIP-free pokeweed and endod suspension culture cells were found to be highly active in vitro, as measured by poly(U)-directed polyphenylalanine synthesis. Phytolacca ribosomes challenged with conspecific RIPs generated dose-response curves (IC50 of 1 nM PAP or dodecandrin) very similar to those from wheat germ ribosomes. To determine if Phytolacca cells produce a cytosolic 'anti-RIP' protective element, ribosomes were combined with Phytolacca postribosomal supernatant factors from culture cells, then challenged with conspecific RIPs. Resulting IC50 values of 3-7 nM PAP, PAP-II, PAP-S or dodecandrin indicate that supernatants from these Phytolacca cells lack a ribosomal protective element. This research demonstrates that PAP inactivates pokeweed ribosomes (and is therefore potentially toxic to pokeweed cells) and supports the local suicide model for PAP's in vivo antiviral mechanism. The importance of spatial separation between PAP and ribosomes of cells producing this RIP is emphasized, particularly if crop plants are transformed with the PAP gene to confer antiviral protection.

Crystal structure of an endochitinase from Hordeum vulgare L. seeds

Higher plants contain multiple constitutively expressed proteins for defense against infection by viruses, bacteria, and fungi. One such class of proteins, the chitinases, are effective antifungal agents because they hydrolyze the insoluble beta-1,4-linked polymer of N-acetylglucosamine (chitin), which is the major component of the mycelial cell wall of many fungi. We report here the three-dimensional, 2.8 A, crystal structure of a 26 kDa endochitinase from barley (Hordeum vulgare L.) seeds. The 243 amino acid residue molecule is rich in alpha-helices and has three disulfide bonds. A prominent elongated cleft runs the length of the molecule, and is presumably the region responsible for substrate binding and catalysis. Endochitinases from various species of plants show a high degree of similarity in their amino acid sequences. It is therefore likely that the barley endochitinase structure can serve as a model for other plant endochitinases and that catalytic models based on that structure will be applicable to the entire enzyme family.

Crystallization of an endochitinase from Hordeum vulgar L. seeds

Higher plants contain several constitutively expressed proteins for protection against infections by viruses, bacteria and fungi. Here we report the crystallization of a polypeptide with antifungal activity, a 26,000 dalton endochitinase from barley (Hordeum vulgare L.) seeds, in a form suitable for high-resolution X-ray analysis. Crystals were grown by vapor diffusion under several different conditions. The best crystals, obtained with ammonium sulfate as the precipitant, belong to the tetragonal space group P4(1)2(1)2 (P4(3)2(1)2), with cell dimensions a = b = 62.9 A and c = 96.0 A. The cell dimensions are consistent with one endochitinase molecule per asymmetric unit, and the crystals diffract to at least 2.0 A resolution.

Structure of a ricin mutant showing rescue of activity by a noncatalytic residue

Ricin A chain is an N-glycosidase which removes a single adenine base from a conservative loop of 28S rRNA, thereby inactivating eukaryotic ribosomes. The mechanism of action has been proposed to include transition-state stabilization of an oxycarbonium ion on the substrate ribose by interaction with Glu 177. Conversion of Glu 177 to Gln reduces activity nearly 200-fold [Ready, M. P., Kim, Y., & Robertus, J. D. (1991) Proteins: Struct., Funct., Genet. 10, 270-278] while conversion to Ala (E177A) reduces activity only 20-fold [Schlossman, D., Withers, D., Welsh, P., Alexander, A., Robertus, J., & Frankel, A. (1989) Mol. Cell. Biol. 9, 5012-5021]. X-ray analysis of the latter mutant protein shows that a residue at the edge of the active site, Glu 208, rotates into the space left vacant by the mutation. Its rearranged carboxylate partially substitutes for that of Glu 177. This is equivalent to the rescue of enzyme activity by a second-site reversion. Kinetic analysis shows the E177A mutation affects kcat and not Km, consistent with the notion that the carboxylate serves in transition-state stabilization.

Crystallographic refinement of ricin to 2.5 A

The plant cytotoxin ricin consists of two disulfide-linked chains, each of about 30,000 daltons. An initial model based on a 2.8 A MIR electron density map has been refined against 2.5 A data using rounds of hand rebuilding coupled with either a restrained least squares algorithm or molecular dynamics (XPLOR). The last model (9) has an R factor of 21.6% and RMS deviations from standard bond lengths and angles of 0.021 A and 4.67 degrees, respectively. Refinement required several peptide segments in the original model to be adjusted translationally along the electron density. A wide range of lesser changes were also made. The RMS deviation of backbone atoms between the original and model 9 was 1.89 A. Molecular dynamics proved to be a very powerful refinement tool. However, tests showed that it could not replace human intervention in making adjustments such as local translations of the peptide chain. The R factor is not a completely satisfactory indicator of refinement progress; difference Fouriers, when observed carefully, may be a better monitor.

Site-directed mutagenesis of ricin A-chain and implications for the mechanism of action

Ricin A-chain is an N-glycosidase that attacks ribosomal RNA at a highly conserved adenine residue. The enzyme is representative of a large family of medically significant proteins used in the design of anticancer agents and in the treatment of HIV infection. The x-ray structure has been used as a guide to create several active site mutations by directed mutagenesis of the cloned gene. Glu177 is a key catalytic residue, and conversion to Gln reduces activity 180-fold. Asn209 is shown to participate in substrate binding by kinetic analysis. Conversion to Ser increases Km sixfold but has no effect on kcat. Conversion of Tyr80 and Tyr123 to Phe decreases activity by 15- and 7-fold respectively. A mechanism of action is proposed that involves binding of the substrate adenine in a syn configuration that resembles the transition state; the putative oxycarbonium ion is probably stabilized by interaction with Glu177.

Ribosome-inhibiting proteins, retroviral reverse transcriptases, and RNase H share common structural elements

Plant ribosome-inhibiting proteins are shown to be homologous at the domain level to RNase H from Escherichia coli and to two regions of the pol gene product of retroviral reverse transcriptases. One of these regions carries the viral integrase or int function, while the other has previously been suggested to contain the viral RNase H exo activity. Several residues conserved among the ribosome inhibitors, E. coli RNase H, and the integrase proteins are seen to occupy a prominent cleft in the tertiary structure of the ribosome inhibitor ricin, suggesting roles in binding or catalysis. It is likely that these homologous sequences represent modern derivatives of an ancient protein-folding unit capable of nucleic acid binding and modification which has been incorporated into a variety of enzyme functions.

Extracellular localization of pokeweed antiviral protein

Pokeweed antiviral protein is an enzyme of Mr 29,000 known to inactivate a wide variety of eukaryotic ribosomes. We have used electron microscopy to show that the antibody specific for the protein is bound within the cell wall matrix of leaf mesophyll cells from Phytolacca americana. Any penetration or breakage of the cell wall and membrane could allow the enzyme to enter the cytoplasm, where it is likely to inhibit protein synthesis in the damaged cell. We speculate that pokeweed antiviral protein is a defensive agent whose principal function is probably antiviral.

Dodecandrin, a new ribosome-inhibiting protein from Phytolacca dodecandra

Dodecandrin, a newly discovered ribosome-inhibiting protein, has been isolated and purified from the leaves of the African endod plant, Phytolacca dodecandra. Dodecandrin has a molecular weight of approx. 29 000. It cross-reacts with antiserum prepared against pokeweed antiviral protein from Phytolacca americana and exhibits similar requirements for antiribosomal activity. It is more basic than pokeweed antiviral protein, and comparison of the first 30 amino-terminal residues of the two proteins reveals 83% homology. This level of homology is greater than that between pokeweed antiviral protein and pokeweed antiviral protein S, another antiviral protein found in P. americana. Such conservatism in sequence, coupled with the high efficiency of the proteins in deactivating ribosomes and with their abundance in plant tissue, suggests that they serve an important function in the life of the plant, probably as a defense against infection.

Ricin B chain and discoidin I share a common primitive protein fold

The galactoside-binding B chain of the cytotoxic protein ricin is apparently derived from a conservative exon-sized 40-residue peptide which is repeated four times in the molecule. A very similar peptide can also be seen in the amino acid sequence of the slime mold lectin discoidin I, which itself appears to be the product of a gene duplication. There is presently no chemical or structural evidence concerning the function of this peptide region. Nevertheless, the size of this unit, its prominence in the structure of ricin B chain, and its apparent conservation in carbohydrate-binding proteins from widely divergent organisms suggest that it may represent an extremely ancient galactoside-binding exon unit.