PDBsum entry: 3b8y

Lyase

PDB id: 3b8y

Contents

Protein chains

304 a.a. *

Ligands

ADA-ADA-ADA-ADA ×2

Metals

_CA

_ZN

Waters ×171

* Residue conservation analysis

PDB id:

3b8y

Name:

Lyase

Title:

Crystal structure of pectate lyase peli from erwinia chrysanthemi in complex with tetragalacturonic acid

Structure:

Endo-pectate lyase. Chain: a, b. Engineered: yes

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Gene: peli. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.30Å R-factor: 0.198 R-free: 0.253

Authors:

C.Creze,S.Castang,E.Derivery,R.Haser,V.Shevchik,P.Gouet

Key ref:

C.Creze et al. (2008). The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate. J Biol Chem, 283, 18260-18268. PubMed id: 18430740 DOI: 10.1074/jbc.M709931200

Date:

02-Nov-07 Release date: 29-Apr-08

Protein chains

O50325  (O50325_ERWCH) -  Endo-pectate lyase (Precursor)

Seq: 344 a.a.

Struc: 304 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.2.2 - Pectate lyase.
• Pathway: Pectin and Pectate Lyases
• Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biochemical function: pectate lyase activity (1 term)

DOI no: 10.1074/jbc.M709931200

J Biol Chem 283:18260-18268 (2008)

PubMed id: 18430740

The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.

C.Creze, S.Castang, E.Derivery, R.Haser, N.Hugouvieux-Cotte-Pattat, V.E.Shevchik, P.Gouet.

ABSTRACT

The crystallographic structure of the family 3 polysaccharide lyase (PL-3) PelI from Erwinia chrysanthemi has been solved to 1.45 A resolution. It consists of an N-terminal domain harboring a fibronectin type III fold linked to a catalytic domain displaying a parallel beta-helix topology. The N-terminal domain is located away from the active site and is not involved in the catalytic process. After secretion in planta, the two domains are separated by E. chrysanthemi proteases. This event turns on the hypersensitive response of the host. The structure of the single catalytic domain determined to 2.1 A resolution shows that the domain separation unveils a "Velcro"-like motif of asparagines, which might be recognized by a plant receptor. The structure of PelI in complex with its substrate, a tetragalacturonate, has been solved to 2.3 A resolution. The sugar binds from subsites -2 to +2 in one monomer of the asymmetric unit, although it lies on subsites -1 to +3 in the other. These two "Michaelis complexes" have never been observed simultaneously before and are consistent with the dual mode of bond cleavage in this substrate. The bound sugar adopts a mixed 2(1) and 3(1) helical conformation similar to that reported in inactive mutants from families PL-1 and PL-10. However, our study suggests that the catalytic base in PelI is not a conventional arginine but a lysine as proposed in family PL-9.

Selected figure(s)

Figure 1.
FIGURE 1. Structural alignment of the catalytic domain of PelI. A, superimposition of the catalytic domain of PelI (blue) with Pel15 (red) (Protein Data Bank code 1EE6 [PDB] ) and PelC (green) (Protein Data Bank code 2EWE). Bound calcium ions are shown in PelI, Pel15, and PelC with blue, red, and green spheres, respectively. The bound sugar in PelC is shown in yellow. The disordered linker in PelI is shown by a dashed line. B, structure-based sequence alignment with secondary structure elements. Top, red and blue triangles indicate the putative catalytic residue of PelI and PelC, respectively. Bottom, green numbers, red stars, and blue circles indicate PelI disulfide bridges, residues at the interdomain interface (contact distances <3.2 Å), and residues coordinated to a Ca^2+ ion, respectively.

Figure 3.
FIGURE 3. Interactions between the tetrasaccharide and the protein. A, in molecule A. B, in molecule B. The moiety Ada1 is at the reducing end (A1 or B1), and the moiety Ada4 is at the non-reducing end (A4 or B4). A yellow arrow symbolizes the proton abstraction at the C[5] atom.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 18260-18268) copyright 2008.

Figures were selected by the author.