Jon D. Robertus

The crystal structure of the antifungal protein zeamatin, a member of the thaumatin-like, PR-5 protein family

The crystal structure of zeamatin, and comparisons within the family, suggest most PR-5 proteins have an electrostatically polarized surface which may be responsible for antifungal activity.

The refined crystal structure of an endochitinasefrom Hordeum vulgare L. seeds at 1.8 Å resolution

Class II chitinases (EC 3.2.1.14) are plant defense proteins. They hydrolyze chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine (NAG), which is a major cell-wall component of many fungal hyphae. We previously reported the three-dimensional structure of the 26 kDa class II endochitinase from barley seeds at 2.8 A resolution, determined using multiple isomorphous replacement (MIR) methods. Here, we report the crystallographic refinement of this chitinase structure against data to 1.8 A resolution using rounds of hand rebuilding coupled with molecular dynamics (X-PLOR). The final model has an R-value of 18.1% for the 5.0 to 1.8 A data shell and 19.8% for the 10.0 to 1.8 A shell, and root-mean-square deviations from standard bond lengths and angles of 0.017 A and 2.88 degrees, respectively. The 243 residue molecule has one beta-sheet, ten alpha-helices and three disulfide bonds; 129 water molecules are included in the final model. We show structural comparisons confirming that chitinase secondary structure resembles lysozyme at the active site region. Based on substrate binding to lysozyme, we have built a hypothetical model for the binding of a hexasaccharide into the pronounced active site cleft of chitinase. This provides the first view of likely substrate interactions from this family of enzymes; the model is consistent with a lysozyme-like mechanism of action in which Glu67 acts as proton donor and Glu89 is likely to stabilize the transition state oxycarbonium ion. These binding site residues, and many hydrophobic residues are conserved in a range of plant chitinases. This endochitinase structure will serve as a model for other plant chitinases, and that catalytic models based on this structure will be applicable to the entire enzyme family.

Purification and properties of a second antiviral protein from Phytolacca americana which inactivates eukaryotic ribosomes.

Abstract A second antiviral protein which inhibits eukaryotic protein synthesis has been purified from Phytolacca americana leaves harvested in the summer. This second pokeweed antiviral protein ( M r 30,000) was found to be slightly larger than the original pokeweed antiviral protein ( M r 29,000) by sodium dodecyl sulfate-polyacrylamide electrophoresis. The two proteins have similar amino acid compositions but yield different peptide distributions upon tryptic hydrolysis and are immunologically distinct. Both proteins are efficient inhibitors of eukaryotic protein synthesis, tobacco mosaic virus transmission, and ribosome-elongation factor interaction. The primary mode of protein synthesis inhibition caused by the two antiviral proteins is the reduction of the ribosomal affinity for elongation factor 2, which results in the inhibition of the translocation step in protein synthesis.

X-ray structure of an anti-fungal chitosanase from streptomyces N174.

We report the 2.4 Å X-ray crystal structure of a protein with chitosan endo-hydrolase activity isolated from Streptomyces N174. The structure was solved using phases acquired by SIRAS from a two-site methyl mercury derivative combined with solvent flattening and non-crystallographic two-fold symmetry averaging, and refined to an R-factor of 18.5%. The mostly α-helical fold reveals a structural core shared with several classes of lysozyme and barley endochitinase, in spite of a lack of shared sequence. Based on this structural similarity we postulate a putative active site, mechanism of action and mode of substrate recognition. It appears that Glu 22 acts as an acid and Asp 40 serves as a general base to activate a water molecule for an SN2 attack on the glycosidic bond. A series of amino-acid side chains and backbone carbonyl groups may bind the polycationic chitosan substrate in a deep electronegative binding cleft.

2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.

Ebulin l is a type‐II ribosome‐inactivating protein (RIP) isolated from the leaves of Sambucus ebulus L. As with other type‐II RIP, ebulin is a disulfide‐linked heterodimer composed of a toxic A chain and a galactoside‐specific lectin B chain. A normal level of ribosome‐inactivating N‐glycosidase activity, characteristic of the A chain of type‐II RIP, has been demonstrated for ebulin l. However, ebulin is considered a nontoxic type‐II RIP due to a reduced cytotoxicity on whole cells and animals as compared with other toxic type‐II RIP like ricin. The molecular cloning, amino acid sequence, and the crystal structure of ebulin l are presented and compared with ricin. Ebulin l is shown to bind an A‐chain substrate analogue, pteroic acid, in the same manner as ricin. The galactoside‐binding ability of ebulin l is demonstrated crystallographically with a complex of the B chain with galactose and with lactose. The negligible cytotoxicity of ebulin l is apparently due to a reduced affinity for galactosides. An altered mode of galactoside binding in the 2γ subdomain of the lectin B chain primarily causes the reduced affinity. Proteins 2001;43:319–326.

Role of arginine 180 and glutamic acid 177 of ricin toxin A chain in enzymatic inactivation of ribosomes.

The gene for ricin toxin A chain was modified by site-specific mutagenesis to change arginine 180 to alanine, glutamine, methionine, lysine, or histidine. Separately, glutamic acid 177 was changed to alanine and glutamic acid 208 was changed to aspartic acid. Both the wild-type and mutant proteins were expressed in Escherichia coli and, when soluble, purified and tested quantitatively for enzyme activity. A positive charge at position 180 was found necessary for solubility of the protein and for enzyme activity. Similarly, a negative charge with a proper geometry in the vicinity of position 177 was critical for ricin toxin A chain catalysis. When glutamic acid 177 was converted to alanine, nearby glutamic acid 208 could largely substitute for it. This observation provided valuable structural information concerning the nature of second-site mutations.

The Structure of an Allosamidin Complex with the Coccidioides immitis Chitinase Defines a Role for a Second Acid Residue in Substrate-assisted Mechanism

Allosamidin is a known inhibitor of class 18 chitinases. We show that allosamidin is a competitive inhibitor of the fungal chitinase CiX1 from Coccidioides immitis, with a K(i) of 60 nM. We report the X-ray structure of the complex and show that upon inhibitor binding the side-chain of Asp169 rotates to form an ion pair with the oxazolinium cation. The mechanism of action is thought to involve protonation of the leaving group by Glu171 and substrate assistance by the sugar acetamido moiety to form an oxazoline-like intermediate. We converted both amino acid residues to the corresponding amide and found that each mutation effectively abolishes enzyme activity. X-ray structures show the mutant enzymes retain the basic wild-type structure and that the loss of mutant activity is due to their altered chemical properties. The high affinity of allosamidin, and its similarity to the putative reaction intermediate, suggests it is a transition state analog. This helps validate our contention that the role of Asp169 is to electrostatically stabilize the reaction transition state.

The Structure of Eukaryotic Translation Initiation Factor-4E from Wheat Reveals a Novel Disulfide Bond

Eukaryotic translation initiation factor-4E (eIF4E) recognizes and binds the m7 guanosine nucleotide at the 5′ end of eukaryotic messenger RNAs; this protein-RNA interaction is an essential step in the initiation of protein synthesis. The structure of eIF4E from wheat (Triticum aestivum) was investigated using a combination of x-ray crystallography and nuclear magnetic resonance (NMR) methods. The overall fold of the crystallized protein was similar to eIF4E from other species, with eight β-strands, three α-helices, and three extended loops. Surprisingly, the wild-type protein did not crystallize with m7GTP in its binding site, despite the ligand being present in solution; conformational changes in the cap-binding loops created a large cavity at the usual cap-binding site. The eIF4E crystallized in a dimeric form with one of the cap-binding loops of one monomer inserted into the cavity of the other. The protein also contained an intramolecular disulfide bridge between two cysteines (Cys) that are conserved only in plants. A Cys-to-serine mutant of wheat eIF4E, which lacked the ability to form the disulfide, crystallized with m7GDP in its binding pocket, with a structure similar to that of the eIF4E-cap complex of other species. NMR spectroscopy was used to show that the Cys that form the disulfide in the crystal are reduced in solution but can be induced to form the disulfide under oxidizing conditions. The observation that the disulfide-forming Cys are conserved in plants raises the possibility that their oxidation state may have a role in regulating protein function. NMR provided evidence that in oxidized eIF4E, the loop that is open in the ligand-free crystal dimer is relatively flexible in solution. An NMR-based binding assay showed that the reduced wheat eIF4E, the oxidized form with the disulfide, and the Cys-to-serine mutant protein each bind m7GTP in a similar and labile manner, with dissociation rates in the range of 20 to 100 s−1.

The structure of ribosome inactivating proteins.

Ribosome Inactivating Proteins, RIPs, depurinate an invariant adenine from the 28S rRNA of eukaryotic ribosomes; they have evolved to near enzymatic perfection for this task. The N-glycosidase fold is conserved in plant and bacterial enzymes. RIPs can form complexes with cell surface recognition proteins that dramatically increase the cytotoxicity of the molecule.

Structure of NS1A effector domain from the influenza A/Udorn/72 virus.

The nonstructural protein NS1A from influenza virus is a multifunctional virulence factor and a potent inhibitor of host immunity. It has two functional domains: an N-terminal 73-amino-acid RNA-binding domain and a C-terminal effector domain. Here, the crystallographic structure of the NS1A effector domain of influenza A/Udorn/72 virus is presented. Structure comparison with the NS1 effector domain from mouse-adapted influenza A/Puerto Rico/8/34 (PR8) virus strain reveals a similar monomer conformation but a different dimer interface. Further analysis and evaluation shows that the dimer interface observed in the structure of the PR8 NS1 effector domain is likely to be a crystallographic packing effect. A hypothetical model of the intact NS1 dimer is presented.