Functional Implications of Structure-Based Sequence Alignment of Proteins in the Extracellular Pectate Lyase Superfamily

Henrissat, Bernard; Heffron, Susan; Yoder, Marilyn D.; Lietzke, S. E.; Jurnak, Frances

doi:10.1104/pp.107.3.963

Cited by 116 publications

(85 citation statements)

References 37 publications

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“…Each oxygen of the carboxylic group of Asp-131 is coordinated to the Ca 2ϩ ion, whereas only one carboxylic oxygen of Asp-129, Glu-166, and Asp-170 is coordinated. Asp-131 is invariant throughout the pectate lyase superfamily (9,37). Asp-129, Glu-166, and Asp-170 are conserved only in the pectate lyase and plant pollen subfamilies.…”

Section: Resultsmentioning

confidence: 99%

Characterization and Implications of Ca2+Binding to Pectate Lyase C

Herron¹,

Scavetta²,

Garrett³

et al. 2003

Journal of Biological Chemistry

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Ca2؉ is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca 2؉ complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca 2؉ concentrations, have been solved and refined at a resolution of 2.2 Å. The Ca 2؉ site represents a new motif for Ca 2؉ , consisting primarily of ␤-turns and ␤-strands. The principal differences between PelC and the PelC-Ca 2؉ structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK a values, the presence of Ca 2؉ and associated structural changes lower the pK a of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca 2؉ affinity for PelC is weak, as the K d was estimated to be 0.132 (؎0.004) mM at pH 9.5, 1.09 (؎0.29) mM at pH 11.2, and 5.84 (؎0.41) mM at pH 4.5 from x-ray diffraction studies and 0.133 (؎0.045) mM at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca 2؉ affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca 2؉ concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca 2؉ ion in PelC has multiple functions.

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Section: Resultsmentioning

confidence: 99%

Characterization and Implications of Ca2+Binding to Pectate Lyase C

Herron¹,

Scavetta²,

Garrett³

et al. 2003

Journal of Biological Chemistry

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“…Surrounding the Ca 2+ site, two invariant Arg residues (Arg-276 and Arg-281) and a Pro residue (Pro-278), thought to make up the pectate-binding site, are also conserved in Banl7. Homology to bacterial pectate lyases also extends to the Asn ladder, which is involved in the stabilization of the parallel /3-strands and to the highly conserved vWiDH cluster (for review, see Henrissat et al [1995]). These structural motifs are shared by pectate lyases from pollen (Wing et al, 1989;Rogers et al, 1992) and style (Budelier et al, 1990.…”

Section: Discussionmentioning

confidence: 99%

“…Notably, these regions are the only sequences that are conserved among all Envinia spp. pectate lyases, and recently have been postulated to encompass the Ca 2+ -binding site and the putative active site of the enzyme (Henrissat et al, 1995;Yoder and Jurnak, 1995).…”

Section: Bafll7mentioning

confidence: 99%

A cDNA Clone Highly Expressed in Ripe Banana Fruit Shows Homology to Pectate Lyases

et al. 1997

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A cDNA clone (Banl7), encoding a protein homologous to pectate lyase, has been isolated from a cDNA library from climacteric banana fruit by means of differential screening. Northern analysis showed that Banl7 mRNA is first detected in early climacteric fruit, reaches a steady-state maximum at the climacteric peak, and declines thereafter in overripe fruit. Accumulation of the Banl7 transcript can be induced in green banana fruit by exogenous application of ethylene. This demonstrates that expression of this gene is under hormonal control, its induction being regulated by the rapid increase in ethylene production at the onset of ripening. The deduced amino acid sequence derived from the Banl7 cDNA shares significant identity with pectate lyases from pollen and plant pathogenic bacteria of the genus Erwinia. Similarity to bacterial pectate lyases that were proven to break down the pectic substances of the plant cell wall suggest that Banl7 might play a role in the loss of mesocarp firmness during fruit ripening.

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“…PL has been extensively studied in pathogenic bacteria, which secreted this enzyme causing depolymerization of pectins in the middle lamella and primary cell walls of higher plants, and consequently the maceration of plant tissues (Henrissat et al, 1995). In bananas, the expression of two distinct PL-like genes (Pel I and Pel II) has been detected during ripening.…”

Section: Pectate Lyasementioning

confidence: 99%

Biochemistry of fruit softening: an overview

Payasi¹,

Mishra

Chaves

et al. 2009

Physiol Mol Biol Plants

205

125

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Softening is a developmentally programmed ripening process, associated with biochemical changes in cell wall fractions involving hydrolytic processes resulting in breakdown of cell-wall polymers such as cellulose, hemicelluloses and pectin etc. Various hydrolytic reactions are brought about by polygalacturonase, pectin methyl esterase, pectate lyase, rhamnogalacturonase, cellulase and β-galactosidase etc. Besides these enzymes, expansin protein also plays an important role in softening. Textural changes during ripening help in determining the shelf life of a fruit. An understanding of these changes would help in formulating procedures for controlling fruit softening vis-à-vis enhancing shelf life of fruits. In the present review an attempt has been made to coalesce recent findings on biochemistry of fruit softening.

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Functional Implications of Structure-Based Sequence Alignment of Proteins in the Extracellular Pectate Lyase Superfamily

Cited by 116 publications

References 37 publications

Characterization and Implications of Ca2+Binding to Pectate Lyase C

Characterization and Implications of Ca2+Binding to Pectate Lyase C

A cDNA Clone Highly Expressed in Ripe Banana Fruit Shows Homology to Pectate Lyases

Biochemistry of fruit softening: an overview

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