The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex

Cho, Sang Woo; Lee, Seungho; Shin, Wonjae

doi:10.1006/jmbi.2001.4919

Cited by 94 publications

(103 citation statements)

References 54 publications

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“…On the other hand, Pectinex contains several enzymes with pectolytic activities including polygalacturonase (product datasheet). As homogalacturonan may represent about 65% of pectins [26] and the main enzyme degrading its backbone is polygalacturonase, the pI of this enzyme (from A. aculeatus) was considered, being in the range 4.2-4.6 [27]. Therefore, all the solutions used for preparing Au-cellulase and -pectinase complexes were adjusted at pH 4.5.…”

Section: Preparation Of the Gold-enzyme Complex And Tissue Labellingmentioning

confidence: 99%

Localization of polysaccharides in isolated and intact cuticles of eucalypt, poplar and pear leaves by enzyme-gold labelling

Guzmán

Fernández

García

et al. 2014

Plant Physiology and Biochemistry

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Section: Preparation Of the Gold-enzyme Complex And Tissue Labellingmentioning

confidence: 99%

Localization of polysaccharides in isolated and intact cuticles of eucalypt, poplar and pear leaves by enzyme-gold labelling

Guzmán

Fernández

García

et al. 2014

Plant Physiology and Biochemistry

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“…EndoPG is an inverting enzyme. 25) As indicated previously, 11,12) the distances between the absolutely conserved three aspartates are 4.4 A (Asp153 Asp173), 5.5 A (Asp153 Asp174), and 4.8 A (Asp173 Asp174), respectively. No conserved acidic residues are found at a distance of about 10 A from each other.…”

Section: Catalytic Mechanismmentioning

confidence: 59%

“…EndoPG I has a right handed helical structure, which is common to the pectinases, such as pectate lyases, 14) rhamnogalacturonase, 13) and endoPG from E. carotovora, 10) A. niger 11) and A. aculeatus 12) (Fig. 3A).…”

Section: )mentioning

confidence: 99%

“…8) Site directed mutagenesis experiments with the fungi Aspergillus niger endoPG II revealed that each of these three aspartate residues is critical for the catalytic function. 9) Recently, the crystal structures of the endoPGs from the bacterium Erwinia carotovora 10) and the fungi Aspergillus niger 11) and A. aculeatus 12) were solved at 1.9, 1.68 and 2.0 A resolutions, respectively. These structures fold into a right handed parallel helix, which is also found in other pectin degrading enzymes, such as rhamnogalacturonase A 13) and pectate lyase.…”

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confidence: 99%

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Reaction Mechanism Based on X-ray Crystallography at Atomic Resolution of Endopolygalacutronase I from Fungus <i>Stereum purpureum</i>

et al. 2004

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The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two Dgalacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one -D-galactopyranuronate, GalpA, was found in the reducing end side of Asp153, Asp173 and Asp174, which are considered as candidates of catalytic residues. This reveals that the position of GalpA is the 1 subsite, thus proving the strong affinity of the 1 subsite expected from the bond cleavage frequency on oligo-galacturonates. In the ternary complex, an additional -Dgalactofuranuronate was found in the 1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the 1 subsite, the carboxy group interacts with three basic residues, His195, Arg226 and Lys228, which were conserved in all endopolygalacturonases. In the 1 subsite, the unique non-prolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. Based on the structures of Galf A and GalpA bound in the ternary complex, a structural model of the di-galacturonic acid part of the substrate molecule bound in both the 1 and 1 subsites across from the catalytic residues was constructed. The di-galacturonate model structure sheds light on the catalytic mechanism. Asp173 is at the appropriate position to be a proton donor to the fissile glycosidic bond. Asp153 or Asp174 seems to act as a general base to abstract a proton from the nucleophilic water.

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“…The three-dimensional structures of several PGs have been reported (Pickersgill et al 1998;van Santen et al 1999;Cho et al 2001;Federici et al 2001;Shimizu et al 2002;van Pouderoyen et al 2003) but only one structure of exopolygalacturonosidase (from Yersinia enterocolitica) with an accompanying explanation of the molecular determinants for its specialized activity (Abbott & Boraston 2007). Tertiary structure of exoPG or generally of any plant pectate hydrolase has not been reported yet.…”

Section: Introductionmentioning

confidence: 99%

Oligogalacturonate hydrolase with unique substrate preference from the pulp of parsley roots

et al. 2009

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Abstract:The main form of pectate hydrolases in the cell wall of parsley roots showed a unique substrate preference of a plant exopolygalacturonase because it clearly preferred the substrates with degree of polymerization about 10. This form was separated from the others, purified and characterized. Enzyme exhibited sharp pH optimum corresponding to pH 4.7, molecular mass 53.5 kDa, and isoelectric point 5.3. It was stable at 50• C in 2-h assay and had optimum of temperature at 60• C (activation energy being 37.0 kJ/mol). The interaction with concanavalin A indicated the glycosylation of enzyme. Substrates were cleaved from the non-reducing end.

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The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex

Cited by 94 publications

References 54 publications

Localization of polysaccharides in isolated and intact cuticles of eucalypt, poplar and pear leaves by enzyme-gold labelling

Localization of polysaccharides in isolated and intact cuticles of eucalypt, poplar and pear leaves by enzyme-gold labelling

Reaction Mechanism Based on X-ray Crystallography at Atomic Resolution of Endopolygalacutronase I from Fungus <i>Stereum purpureum</i>

Oligogalacturonate hydrolase with unique substrate preference from the pulp of parsley roots

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