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

Abstract

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.

Figure 1

Five examples of plant cell wall degradative enzymes that fold into a parallel β helix motif. The predominant secondary structural features of the proteins are illustrated as β strands, and the coils represent α helices. (A) E. chrysanthemi pectate lyase C. (B) E. chrysanthemi pectate lyase E. (C) A. niger pectin lyase B. (D) E. carotovora polygalacturonase. (E) A. aculeatus rhamnogalacturonase A.

Figure 2

Schematic diagram of α-1,4-polygalacturonic acid cleavage by a β-elimination mechanism. The pectate lyases are expected to contribute a minimum of three groups to the catalytic mechanism: P⁺, which neutralizes the charge on the carboxylic acid group; B, a general base that abstracts the proton from C-5; and A, which is involved in the transfer of the final proton to the glycosidic oxygen, leaving a double bond between C-4 and C-5.

Figure 3

Stereoview of the PelC locations of 10 invariant amino acids within the extracellular pectate lyase superfamily. The two clusters of invariant amino acids are located on opposite sides of the parallel β helix, separated by approximately 25 Å across the diameter and by approximately 90 Å around the circumference of the parallel β helix. The α-carbon backbone of PelC is illustrated as a green ribbon and the Ca²⁺ ions as yellow spheres. The invariant amino acids are labeled at the α-carbon and are represented by rods using the International Union of Pure and Applied Chemistry coloring code: carbon atoms are gray; oxygen atoms, red; and nitrogen atoms, blue.

Figure 4

Stereoview of the active site of the PelC R218K-(Ca²⁺)₄-pentaGalpA complex. The color code is the same as that used in Fig. 3.

Figure 5

Overview of the PLB-(mGalpA)₄ model. Pectin lyase B is shown as yellow ribbons. The substrate and the interacting amino acids are represented by rods using the color code described in Fig. 3.

Figure 6

Stereoview of the active site of the PLB-(mGalpA)₄ model. The view of the active site is the same as that used in Fig. 4 to allow for comparisons. The hydrophobic pockets around three of the four methyl groups esterified to the uronate moieties are visible. The color code is the same as that used in Fig. 6.

Figure 7

Schematic representation of the pectin lyase B with (GalpA)₄ at a distance of ≤3.0 Å. mGalpA (1) is the reducing saccharide and mGalpA (4) is the nonreducing terminus. Hydrogen bonds are represented with dotted lines and hydrophobic interactions, with boldface lines. Oxygen atoms and methyl groups are represented by circles, with the corresponding number, and the carbon atoms are assumed at the intersection of bonds designated in boldface lines.