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Structure and Topological Symmetry of the Glyphosate Target 5-Enol- Pyruvylshikimate-3-Phosphate Synthase: a Distinctive Protein

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Structure and Topological Symmetry of the Glyphosate Target 5-Enol- Pyruvylshikimate-3-Phosphate Synthase: a Distinctive Protein Proc. Nati. Acad. Sci. USA Vol. 88, pp. 5046-5050, June 1991 Biochemistry Structure and topological symmetry of the glyphosate target 5-enol- pyruvylshikimate-3-phosphate synthase: A distinctive protein fold (x-ray crystallography/aromatic amino acid biosynthesis/herbicide/helical macrodipole) WILLIAM C. STALLINGS*, SHERIN S. ABDEL-MEGUID*, Louis W. LIM*, HUEY-SHENG SHIEH*, HENRY E. DAYRINGER*, NANCY K. LEIMGRUBER*, RODERICK A. STEGEMAN*, KAREN S. ANDERSONt, JAMES A. SIKORSKIt, STEPHEN R. PADGETTEt, AND GANESH M. KISHOREt *Monsanto Corporate Research and tTechnology Division of Monsanto Agricultural Company, Monsanto Company, 700 Chesterfield Village Parkway, St. Louis, MO 63198 Communicated by J. E. Varner, January 28, 1991 ABSTRACT 5-enol-Pyruvylshikimate-3-phosphate syn- plants has been demonstrated to confer tolerance to the herbi- thase (EPSP synthase; phosphoenolpyruvate:3-phosphoshiki- cide (7). The P101S EPSP synthase from Salmonella typhimu- mate 1-carboxyvinyltransferase, EC 2.5.1.19) is an enzyme on rium shows a 3-fold increase in K, forglyphosate (8, 9), but most the pathway toward the synthesis of aromatic amino acids in glyphosate-tolerant EPSP synthases have a significant alter- plants, fungi, and bacteria and is the target of the broad- ation in Km for PEP; for example, the Ki for glyphosate of the spectrum herbicide glyphosate. The three-dimensional structure G96A Escherichia coli (SM-1) variant is increased 8000-fold of the enzyme from Escherchia coli has been determined by relative to the wild-type enzyme, and this is accompanied by crystallographic techniques. The polypeptide backbone chain 13-fold increase in Km for PEP (5). An EPSP synthase variant was traced by examination ofan electron density map calculated ideal for genetically engineering glyphosate tolerance in crop at 3-A resolution. The two-domain structure has a distinctive plants would have no alteration in kcat and Km for substrates and fold and appears to be formed by 6-fold replication of a protein >10-fold enhancement in the Ki for glyphosate. folding unit comprising two parallel helices and a four-stranded EPSP synthase has been extensively investigated by using sheet. Each domain is formed from three of these units, which chemical and biophysical approaches (10-16); correlation of are related by an approximate threefold symmetry axis; in each these data with the three-dimensional structure ofthe enzyme domain three of the helices are completely buried by a surface is essential for a detailed description of the reaction mecha- formed from the three a-sheets and solvent-accessible faces of nism and its inhibition by glyphosate. Understanding how the other three helices. The domains are related by an approx- substrates and the inhibitor, glyphosate, bind to EPSP syn- imate dyad, but in the present crystals the molecule does not thase would facilitate both the design of glyphosate-tolerant display pseudo-symmetry related tothe symmetry ofpoint group variants and the targeted synthesis of new herbicides. As a 32 because its approximate threefold axes are almost normal. A first step toward understanding the interaction of glyphosate possible relation between the three-dimensional structure of the with EPSP synthase, we have crystallized the enzyme from protein and the linear sequence ofits gene will be described. The E. coli and determined its structure at 3-A resolution.§ topological threefold symmetry and orientation of each of the two observed globular domains may direct the binding of METHODS substrates and inhibitors by a helix macrodipole effect and E. coli EPSP synthase was isolated from a cloned E. coli implies that the active site is located near the interdomain strain that overproduces the protein, and the enzyme was crossover segments. The structure also suggests a rationale for purified as described (18, 19). Crystals were grown by the the glyphosate tolerance conferred by sequence alterations. method of vapor diffusion in sitting or hanging drops (20) by using 35-45% saturated ammonium sulfate buffered at pH Herbicides have become an integral part ofmodem agriculture 7.5-8.5 with 100 mM Tris as the precipitant. The protein providing cost-effective and reliable weed control during crop concentration was adjusted to 15 mg/ml in 29 mM 2-mer- production. The herbicide Round-up (Monsanto) has outstand- captoethanol buffered at pH 7.5 with 10 mM Tris. The ing toxicological, environmental, and herbicidal properties (1, enzyme crystallizes in the orthorhombic space group P212121 2). Glyphosate, its active ingredient, inhibits 5-enol-pyru- with a = 92.1, b = 83.2, and c = 71.7 A and with one molecule vylshikimate-3-phosphate synthaset (EPSP synthase; phos- of the monomeric protein in the crystallographic asymmetric phoenolpyruvate:3-phosphoshikimate 1-carboxyvinyltrans- unit. X-ray diffraction data were measured from native and ferase, EC 2.5.1.19), an enzyme leading to the biosynthesis of derivative crystals with a dual chamber multiwire detector aromatic compounds in plants and microbes. EPSP synthase system (21). The structure was determined by the multiple- catalyzes an unusual, reversible condensation of shikimate isomorphous replacement method (22) using five mercurial 3-phosphate (S3P) and phosphoenolpyruvate (PEP) with trans- derivatives (22, ¶) that all bind at three sites with varying fer ofthe carboxyvinyl moiety from PEP to S3P. Glyphosate is a competitive inhibitor with respect to PEP and an uncompet- Abbreviations: EPSP synthase, 3-enol-pyruvylshikimate-5-phosphate itive inhibitor with respect to S3P (3, 4). synthase; S3P, shikimate 3-phosphate; PEP, phosphoenolpyruvate. tOfficial enzyme nomenclature renumbers the Shikimate ring in the Introduction of glyphosate tolerance into crop plants is of reverse direction; hence the systematic name exchanges the substitu- significant academic and commercial interest (5). Recent de- ents at positions 3 and 5. velopments in plant genetic engineering permit the introduction §The atomic coordinates have been deposited in the Protein Data and expression of genes in a wide range of crop plants (6). Bank (17), Chemistry Department, Brookhaven National Labora- Expression of glyphosate-tolerant EPSP synthase variants in tory, Upton, NY 11973 (reference code lEPS). $The five heavy atom derivatives were prepared by soaking native EPSP synthase crystals in 1 mM ethyl mercurithiosalicylate, 1 mM methyl The publication costs of this article were defrayed in part by page charge mercury (II) chloride, 1 mM mercury (II) acetate, saturated mercuri- payment. This article must therefore be hereby marked "advertisement" phenyl glyoxal, and saturated dimercuriacetate (23). The latterwas a gift in accordance with 18 U.S.C. §1734 solely to indicate this fact. from Robert Fletterick of the University of California, San Francisco. 5046 Downloaded by guest on September 24, 2021 Biochemistry: Stallings et al. Proc. Natl. Acad. Sci. USA 88 (1991) 5047 occupancies. The resulting electron density map was further synthase structure; the strand corresponding to strand e in improved by using the density modification procedure de- Fig. 3 Left is missing. Folding units 2 and 3, although scribed by Wang (24) with 0.84 as the figure-of-merit of the complete, are formed from discontinuous polypeptide chain solvent-leveled map. segments (Fig. 4). The backbone chain fold ofEPSP synthase is therefore not RESULTS AND DISCUSSION that of a simple symmetric molecule formed by sequential repetition of a folding motif. Were this the case, it would be The chain tracing of a single molecule of E. coli EPSP elegant to imagine that the structure had evolved via 6-fold synthase is illustrated in Fig. 1. The structure consists oftwo replication of a primordial gene for the folding unit. As distinct globular domains, which are roughly hemispheric, explained below, however, close examination of the order in each with a radius of about 25 A. Both the amino and the which the secondary structural elements of the folding units carboxyl terminus of the chain are located in the lower occur along the sequence suggests that such a mechanism is domain with two polypeptide crossover segments clearly still defined in the electron density possible. In Fig. 3 Left, the strands and helices of the 3-A map. Distributed about folding unit are assigned letters a through f in the order in the axis of each hemisphere are three buried parallel helices which of three to four turns each; the domain surfaces comprise they appear in each of the three examples connected three 3-sheets, most with four strands, and three parallel by continuous polypeptide chain. In Fig. 4 Right, the ele- helices that have solvent accessible faces. These constitute ments of secondary structure are expressed in the order in the principal elements of secondary structure in the EPSP which they appear along the chain of the folded protein. synthase molecule. The backbone folds of the two domains Although the elements ofsecondary structure offolding units are therefore remarkably similar. Superposition of a-carbon 2 and 3 are from discontinuous segments of the chain (Fig. 4 atoms from one domain on those of the other yields a 2.1-A Left), in the coding segment of the gene of E. coli EPSP rms deviation when 131 atoms (of 208 atoms in each domain) synthase they arejoined by the two pentapeptide interdomain are considered equivalent and used in the least-squares crossover segments (Fig. 4 Right). At the first crossover, the calculation of the transformation matrix (26). These results union of the amino terminus of unit 2 and the carboxyl initially suggested that EPSP synthase is the product ofgene terminus of unit 3 yields continuous expression of secondary duplication. However, the structure displays higher than structural elements a through f. Likewise, crossback from twofold topological symmetry. folding unit 3 to unit 2 is also accomplished with related As shown in Fig. 2, in each domain an approximate continuity. threefold axis of symmetry relates the principal elements of Consistent with the blocking shown in Fig. 4 Right, the secondary structure and generates three subdomains or pro- discontinuous DNA coding sequences for folding units 2 and tein folding units.
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