The Three-Dimensional Structure of Aspergillus niger Pectin Lyase B at 1.7-Å Resolution1

Pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the Northern Hemisphere. We report the first crystal structure of a cedar allergen, Jun a 1, from the pollen of the mountain cedar Juniperus ashei (Cupressaceae). The core of the structure consists primarily of a parallel ␤-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms. Four IgE epitopes mapped to the surface of the protein are accessible to the solvent. The conserved vWiDH sequence is covered by the first 30 residues of the N terminus. The potential reactive arginine, analogous to the pectin/pectate lyase reaction site, is accessible to the solvent, but the substrate binding groove is blocked by a histidine-aspartate salt bridge, a glutamine, and an ␣-helix, all of which are unique to Jun a 1. These observations suggest that steric hindrance in Jun a 1 precludes enzyme activity. The overall results suggest that it is the structure of Jun a 1 that makes it a potent allergen.

Section: Resultsmentioning

confidence: 72%

“…6). In addition, the side chain of this putative reactive arginine is extended in the same direction as all of the equivalent arginines in the other Pnl (16,35) and Pel (17,19,21,34).…”

Section: Resultsmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Crystal Structure of Jun a 1, the Major Cedar Pollen Allergen from Juniperus ashei, Reveals a Parallel β-Helical Core

Czerwinski

Midoro-Horiuti

White

et al. 2005

“…These characteristics of lyases indicate that they share common structural features determining their uronate recognition sites and reaction modes (␤-elimination reaction). Although structural analyses of lyases for pectate (3)(4)(5)(6)(7)(8), alginate (9), hyaluronate (10,11), and chondroitin (12,13) have been made, there is little information regarding the structural rules common to polysaccharide lyases.…”

mentioning

confidence: 99%

Crystal Structure of Bacillus sp. GL1 Xanthan Lyase, Which Acts on the Side Chains of Xanthan

Hashimoto¹,

Nankai²,

Mikami³

et al. 2003

Xanthan lyase, a member of polysaccharide lyase family 8, is a key enzyme for complete depolymerization of a bacterial heteropolysaccharide, xanthan, in Bacillus sp. GL1. The enzyme acts exolytically on the side chains of the polysaccharide. The x-ray crystallographic structure of xanthan lyase was determined by the multiple isomorphous replacement method. The crystal structures of xanthan lyase and its complex with the product (pyruvylated mannose) were refined at 2.3 and 2.4 Å resolution with final R-factors of 17.5 and 16.9%, respectively. The refined structure of the product-free enzyme comprises 752 amino acid residues, 248 water molecules, and one calcium ion. The enzyme consists of N-terminal ␣-helical and C-terminal ␤-sheet domains, which constitute incomplete ␣ 5 /␣ 5 -barrel and anti-parallel ␤-sheet structures, respectively. A deep cleft is located in the N-terminal ␣-helical domain facing the interface between the two domains. Although the overall structure of the enzyme is basically the same as that of the family 8 lyases for hyaluronate and chondroitin AC, significant differences were observed in the loop structure over the cleft. The crystal structure of the xanthan lyase complexed with pyruvylated mannose indicates that the sugar-binding site is located in the deep cleft, where aromatic and positively charged amino acid residues are involved in the binding. The Arg 313 and Tyr 315 residues in the loop from the N-terminal domain and the Arg 612 residue in the loop from the C-terminal domain directly bind to the pyruvate moiety of the product through the formation of hydrogen bonds, thus determining the substrate specificity of the enzyme.

“…The structure and function relationships of polygalacturonan-degrading enzymes, including hydrolases and lyases have also been well documented (13)(14)(15)(16)(17)(18)(19)(20). However, little information is available on the degradation of RG regions by microbes except for Aspergillus species (21) and Erwinia chrysanthemi (22,23).…”

mentioning

confidence: 99%

A Novel Structural Fold in Polysaccharide Lyases

Ochiai

Itoh

Maruyama

et al. 2007

Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls. An extracellular RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG type-I through a ␤-elimination reaction. Crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, were determined at 1.4 and 2.5 Å resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed ␤-propeller with a deep cleft in the center as a basic scaffold, and its structural fold has not been seen in polysaccharide lyases analyzed thus far. Structural analysis of the disaccharide-bound YesW and a site-directed mutagenesis study suggested that Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In addition to amino acid residues binding to the disaccharide, one calcium ion, which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the enzyme activity. This is, to our knowledge, the first report of a new structural category with a ␤-propeller fold in polysaccharide lyases and provides structural insights into substrate binding by RG lyase.Plant cell wall degradation is essential for plant pathogenic and saprophytic microbes to invade plants. The plant cell wall mainly consists of polysaccharides and proteins, with polysaccharides being more abundant. These polysaccharides are divided into three groups, cellulose, hemicellulose, and pectin (1). Pectin is more soluble in water than cellulose and hemicellulose, suggesting that this polysaccharide is the preferred target for plant-associated microbes. Pectin is further divided to three regions, i.e. polygalacturonan, rhamnogalacturonan type-I (RG-I), 2 and rhamnogalacturonan type-II (RG-II). In pectin molecules, polygalacturonan is present as a linear backbone, and RG-I and RG-II are attached to the backbone as branched chains (2-4). RG-I is a polymer with a disacchariderepeating unit consisting of L-rhamnopyranose and D-galactopyranouronic acid (GalA) as a main chain, and arabinans and galactans are attached to the main chain (5). RG-II has a backbone of polygalacturonan, and its side chains consist of a complex of ϳ30 monosaccharides, including rare sugars such as apiose and aceric acid (6). These plant cell wall polysaccharides become substrates to be degraded through reactions of polysaccharide hydrolases and/or lyases produced by plant pathogenic and saprophytic microbes. Hydrolases cleave glycoside bonds in polysaccharides via hydrolysis, and lyases do so by ␤-elimination reactions (7,8).The degradation pathway for the polygalacturonan region has been characterized extensively in microbes (9 -12). The structure and function relationships of polygalacturonan-degrading enzymes, including hydrolases and lyases have also been well documented (13)(...