Structure of Xyloglucan Xylosyltransferase 1 Reveals Simple Steric Rules That Define Biological Patterns of Xyloglucan Polymers
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Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers Alan T. Culbertsona, Jacqueline J. Ehrlicha, Jun-Yong Choeb, Richard B. Honzatkoa, and Olga A. Zabotinaa,1 aRoy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011; and bDepartment of Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064 Edited by Kenneth Keegstra, Michigan State University, East Lansing, MI, and approved April 27, 2018 (received for review January 19, 2018) The plant cell wall is primarily a polysaccharide mesh of the most substrates, including, carbohydrates, proteins, and lipids (12). abundant biopolymers on earth. Although one of the richest Amino acid sequences in the Carbohydrate Active Enzyme Da- sources of biorenewable materials, the biosynthesis of the plant tabase fall into 105 families of GTs (13, 14). Available structures polysaccharides is poorly understood. Structures of many essential indicate most GT families adopt one of two folds, GT-A or GT- plant glycosyltransferases are unknown and suitable substrates B, although a rarer GT-C fold has been proposed (12). The GT- are often unavailable for in vitro analysis. The dearth of such A fold has two Rossmann-like domains that form a central information impedes the development of plants better suited for β-sheet, each face of which is covered by α-helices. These are industrial applications. Presented here are structures of Arabidop- typically metal-dependent enzymes that require an Asp-X-Asp sis xyloglucan xylosyltransferase 1 (XXT1) without ligands and in motif for metal coordination (15, 16). GT-B folds also have two complexes with UDP and cellohexaose. XXT1 initiates side-chain Rossmann-like domains, less tightly associated than those of GT- extensions from a linear glucan polymer by transferring the xylo- A folds, with the active site located between domains. GTs are syl group from UDP-xylose during xyloglucan biosynthesis. XXT1, also classified by the stereochemistry of the glycosidic bond in a homodimer and member of the GT-A fold family of glycosyl- the product (inverted or retained) relative to that of the sub- transferases, binds UDP analogously to other GT-A fold enzymes. strate (12). The catalytic mechanism of inverting GTs likely follows the single displacement mechanism of inverting glycosyl Structures here and the properties of mutant XXT1s are consistent hydrolases (12, 17). The catalytic mechanism of retaining GTs, with a SN -like catalytic mechanism. Distinct from other systems is i first proposed as a double displacement mechanism similar to the recognition of cellohexaose by way of an extended cleft. The retaining glycosyl hydrolases, has fallen into disfavor due to the XXT1 dimer alone cannot produce xylosylation patterns observed absence of a suitably placed catalytic base and the failure to trap for native xyloglucans because of steric constraints imposed by the a glycosyl-enzyme intermediate. Instead, retaining GTs may acceptor binding cleft. Homology modeling of XXT2 and XXT5, the employ a SNi-like mechanism that consists of the acceptor sub- other two xylosyltransferases involved in xyloglucan biosynthesis, strate approaching from the same face as the leaving group with reveals a structurally altered cleft in XXT5 that could accommodate an oxocarbenium-ion intermediate (18–20). Although structural a partially xylosylated glucan chain produced by XXT1 and/or information is abundant for glycosyltransferases (21), structural XXT2. An assembly of the three XXTs can produce the xylosylation information specifically for GTs involved in plant cell wall patterns of native xyloglucans, suggesting the involvement of an polysaccharide biosynthesis is available only for xyloglucan organized multienzyme complex in the xyloglucan biosynthesis. Significance glycosyltransferases | plant cell wall | xyloglucan The recalcitrant nature of the plant cell wall presents a signif- lant cell walls consist of cellulose, hemicellulose, pectin, and icant challenge in the industrial processing of biomass. Poor Plignin, all of which confer mechanical properties to plant understanding of plant polysaccharide biosynthesis impedes structures, and are important for shape and development. Plant efforts to engineer cell walls susceptible to efficient and un- cell walls represent the largest pool of renewable carbohydrate natural pathways of degradation. Despite numerous genetic and the potential to support numerous industrial applications in and in vitro studies of the xyloglucan xylosyltransferases bioenergy and biomaterials (1, 2). The complex structure of plant (XXT1, XXT2, and XXT5), the specific roles of each in the xylo- lignocellulosic biomass resists enzymatic and microorganism sylation of the xyloglucan backbone is unclear. On the basis of degradation (3). Engineering a biologically viable plant suscep- steric constraints imposed by the active-site cleft of structures tible to enzymatic or nonbiological degradation requires a presented here, we propose a multienzyme complex capable of complete understanding of plant cell wall polysaccharide bio- producing the xylosylation patterns of native xyloglucans. This synthesis and structure. model significantly extends our limited understanding of Xyloglucan (XyG) is the most abundant hemicellulose in the branched polysaccharide biosynthesis. primary cell wall of dicotyledonous plants and has many pro- posed structural and regulatory functions (4–7). XyG consists of Author contributions: A.T.C., R.B.H., and O.A.Z. designed research; A.T.C. and J.J.E. per- a 1,4-β-linked glucan backbone branched with various glycosyl formed research; A.T.C., J.-Y.C., and R.B.H. performed experimental phasing; A.T.C., residues depending on species or tissue (8). The nomenclature R.B.H., and O.A.Z. analyzed data; and A.T.C., J.-Y.C., R.B.H., and O.A.Z. wrote the paper. for XyG structure is as follows: G represents an unbranched The authors declare no conflict of interest. glucose unit, whereas X, L, and F are glucosyl units with Xyl, This article is a PNAS Direct Submission. Gal-Xyl, or Fuc-Gal-Xyl side chains, respectively (9). Arabidopsis Published under the PNAS license. XyG consists of a glucan backbone branched with 1,6-α-linked D- Data deposition: The atomic coordinates and structure factors have been deposited in the Xyl residues, resulting in XXXG-type pattern, which can be Protein Data Bank, www.wwpdb.org (PDB ID codes 6BSU, 6BSV, and 6BSW). further decorated (10, 11). 1To whom correspondence should be addressed. Email: [email protected]. Glycosyltransferases (GTs) catalyze the formation of glyco- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. sidic bonds by transferring a sugar moiety from an activated 1073/pnas.1801105115/-/DCSupplemental. donor, typically a nucleotide sugar, to a variety of acceptor Published online May 21, 2018. 6064–6069 | PNAS | June 5, 2018 | vol. 115 | no. 23 www.pnas.org/cgi/doi/10.1073/pnas.1801105115 Downloaded by guest on September 28, 2021 ABXXT2 when expressed in Drosophila cells (32). The structure of the enzyme (in crystals of space group P212121) was solved by single-wavelength anomalous diffraction (SAD), using data from 2+ a crystal derivatized with K2HgI4. The complex of UDP/Mn (hereafter, the binary complex) and the complex of cellohexaose/ + UDP/Mn2 (hereafter the ternary complex) were formed by li- + gand soaks. XXT1 exhibits highest activity with Mn2 (32), which was included in all ligand soaks. A second crystal form of the apoenzyme (space group C2221), diffracting to 1.5-Å resolution, was solved by molecular replacement. Given its superior reso- lution, the apoenzyme in space group C2221 is reported in SI Appendix, Table S1. Regardless of crystal form, the asymmetric CDunit has two subunits of XXT1, and for each, residues 45– 115 from the N terminus and residues 454–460 from the C ter- minus are without electron density. The purified protein has an observed mass consistent with that expected for residues 45–460. Finally, a substantial void exists in both crystal forms that could accommodate 70 additional residues. XXT1 adopts a GT-A fold with a central β-sheet having both faces covered by α-helices (Fig. 1 A and C). The central β-sheet contains strands β2, β1, β3, β6, β5, and β7, all of which are par- Fig. 1. Structure overview of XXT1. (A) XXT1 monomer (chain A) colored allel except for strand β6 (Fig. 1 A and C). The loops extending blue to red from N to C terminus, respectively. (B) Secondary and tertiary from this central β-sheet and surrounding α-helices define the structure of XXT1. Names of α-helices and β-strands correspond to those in A. active site of XXT1, containing the Asp-X-Asp motif (site of + (C) XXT1 dimer with UDP and cellohexaose. Monomers are shown in green Mn2 binding), donor substrate binding site, and acceptor and yellow. UDP binds to both monomers, whereas cellohexaose binds to binding site (Fig. 1A). The active site is a cleft roughly 13 Å wide only one monomer. (D) View down the symmetry axis of the dimer, 90° and 30 Å long (Fig. 1A). rotation of the molecule shown in C. XXT1 Forms a Dimer. XXT1 forms a dimer with an interface of 2 fucosyltransferase 1 (FUT1), which adds fucose to the terminal roughly 2,900 Å (PDBe PISA; www.ebi.ac.uk/pdbe/pisa/). position of XyG side chains (22, 23). XXT1 dimer has a mass of 96.7 kDa based on amino acid se- Xylosylation of the 6-hydroxyl group of glucose, catalyzed by quence relative to 102.7 kDa determined by gel filtration against xyloglucan xylosyltransferases (XXTs), is the first step in building protein standards of known mass. The high value from gel fil- branches on the XyG backbone (8, 24). XXTs are type II tration is consistent with an increased radius of gyration due to the aforementioned loose stem region of 70 residues (SI Ap- transmembrane enzymes, having a short cytosolic N-terminal pendix A B region, a transmembrane domain, a stem region, and a large , Fig.