Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases

Mayans, Olga; Scott, M.; Connerton, Ian F.; Gravesen, T.; Benen, J.A.E.; Visser, Jaap; Pickersgill, Richard W.; Jenkins, John A.

doi:10.1016/s0969-2126(97)00222-0

Cited by 184 publications

(161 citation statements)

References 28 publications

Supporting

Mentioning

152

Contrasting

Unclassified

Order By: Relevance

“…Two different approaches are employed to neutralize the negative charge on the carboxylic group. Pectin lyase utilizes a Ca 2+ ion to weaken the negative charge (Mayans et al, 1997) while others like HepII (Shaya et al, 2006) and ChonAC (Lunin et al, 2004) exert their asparagine residue to achieve the process. In our model, HepIII likely implements a similar strategy as ChonAC and HepII to accomplish the neutralization by employing its residue Asn260.…”

Section: Discussionmentioning

confidence: 99%

Structural basis of heparan sulfate-specific degradation by heparinase III

Dong¹,

Lu²,

McKeehan³

et al. 2012

Protein Cell

View full text Add to dashboard Cite

Heparinase III (HepIII) is a 73-kDa polysaccharide lyase (PL) that degrades the heparan sulfate (HS) polysaccharides at sulfate-rare regions, which are important co-factors for a vast array of functional distinct proteins including the well-characterized antithrombin and the FGF/FGFR signal transduction system. It functions in cleaving metazoan heparan sulfate (HS) and providing carbon, nitrogen and sulfate sources for host microorganisms. It has long been used to deduce the structure of HS and heparin motifs; however, the structure of its own is unknown. Here we report the crystal structure of the HepIII from Bacteroides thetaiotaomicron at a resolution of 1.6 Å. The overall architecture of HepIII belongs to the (α/α)5 toroid subclass with an N-terminal toroid-like domain and a C-terminal β-sandwich domain. Analysis of this high-resolution structure allows us to identify a potential HS substrate binding site in a tunnel between the two domains. A tetrasaccharide substrate bound model suggests an elimination mechanism in the HS degradation. Asn260 and His464 neutralize the carboxylic group, whereas Tyr314 serves both as a general base in C-5 proton abstraction, and a general acid in a proton donation to reconstitute the terminal hydroxyl group, respectively. The structure of HepIII and the proposed reaction model provide a molecular basis for its potential practical utilization and the mechanism of its eliminative degradation for HS polysaccarides.

show abstract

Section: Discussionmentioning

confidence: 99%

Structural basis of heparan sulfate-specific degradation by heparinase III

Dong¹,

Lu²,

McKeehan³

et al. 2012

Protein Cell

View full text Add to dashboard Cite

show abstract

“…Pectin lyases share a similar enzymatic mechanism with the pectate lyases but recognize a different substrate, that of pectin, the fully methylated, neutral form of pectate. Given the sequence and functional similarities, it is not surprising that the two known pectin lyase structures, PLA (18) and PLB (19), are homologous to the pectate lyases. However, no structural complexes containing pectin are currently available.…”

Section: Model Of the Plb-mgalpa 4 Complexmentioning

confidence: 99%

Structure and function of pectic enzymes: Virulence factors of plant pathogens

Herron

Benen

Scavetta

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

194

130

View full text Add to dashboard Cite

The structure and function of Erwinia chrysanthemi pectate lysase C, a plant virulence factor, is reviewed to illustrate one mechanism of pathogenesis at the molecular level. Current investigative topics are discussed in this paper. P lant cell walls are primarily polysaccharide in composition. A simple but major pathogenic mechanism in plants involves degradation of the cell wall by a battery of polysaccharidases secreted by pathogens. Most of the degradative enzymes are glycoside hydrolases, which degrade the cellulose and pectate matrices by the addition of water to break the glycosidic bonds. The pectate network is also degraded by polysaccharide lyases, which cleave the glycosidic bonds via a ␤-elimination mechanism. To better understand the latter virulence mechanism, research has been carried out on pectate lyase C, a pectolytic enzyme secreted by the pathogenic bacterium Erwinia chrysanthemi. The story of pectate lyase C illustrates how structural techniques have contributed to a detailed understanding of polysaccharide recognition and the lyase cleavage mechanism. In the process, a novel protein structural fold and a unique catalytic role for an arginine have been discovered. The structural results have also provided the first atomic description of a pectate fragment, which differs considerably from the popular view in conformation as well as the mode of interactions with Ca 2ϩ ions. Finally, the growing structural database of pectolytic enzymes is enabling researchers to elucidate subtle structural differences that are responsible for the specific recognition of a unique oligosaccharide sequence from a heterogeneous mix in the plant cell wall. Such knowledge will ultimately lead to a better understanding of the characteristics that render the host susceptible to attack by a particular pathogen.

show abstract

“…Crystal structures of lyases belonging to families PL-1, -3, -4, -5, -6, -7, -8, -9, -10, -16, and -18 have been determined. These enzymes are grouped into six structural categories: (i) the parallel ␤-helix in PL-1 (13,14,16,17,55,56), -3 (57), -6 (58), and -9 (20); (ii) the ␣/␣-barrel in PL-5 (59) and -10 (60, 61); (iii) the ␣/␣-barrel plus anti-parallel ␤-sheet in PL-8 (29,(62)(63)(64)(65)(66); (iv) the ␤-sandwich plus ␤-sheet in PL-4 (33); (v) the ␤-jelly roll in PL-7 (27,67,68) and -18; and (vi) the triplestrand ␤-helix in PL-16 (69). The folds and substrates of polysaccharide lyases are summarized in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…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%

“…These characteristics of lyases indicate that they share common structural features determining uronate recognition and reaction manner (␤-elimination). Crystal structures of polysaccharide lyases in 11 families have been determined thus far (Table 1), and structure and function relationships of enzymes such as lyases for pectate, pectin, alginate, chondroitin, hyaluronan, and xanthan are being analyzed (15,16,(27)(28)(29)(30)(31)(32). However, little knowledge has been accumulated on the mechanisms of substrate recognition and catalytic reaction of RG lyases.…”

mentioning

confidence: 99%

See 1 more Smart Citation

A Novel Structural Fold in Polysaccharide Lyases

Ochiai

Itoh

Maruyama

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

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)(...

show abstract

Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases

Cited by 184 publications

References 28 publications

Structural basis of heparan sulfate-specific degradation by heparinase III

Structural basis of heparan sulfate-specific degradation by heparinase III

Structure and function of pectic enzymes: Virulence factors of plant pathogens

A Novel Structural Fold in Polysaccharide Lyases

Contact Info

Product

Resources

About