alpha-1,4-D-endopolygalacturonic acid lyase
endo-alpha-1,4-polygalacturonic acid lyase
Pentose and glucuronate interconversions
ASP 184;ASP 223;ASP 227(Calcium binding)
ASP 144;ASP 184;ASP 188(Calcium binding)
New domain motif: the structure of pectate lyase C, a secreted plant virulence factor.
The structure of Bacillus subtilis pectate lyase in complex with calcium.
Protein motifs. 3. The parallel beta helix and other coiled folds.
The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
Role of lysine, tryptophan and calcium in the beta-elimination activity of a low-molecular-mass pectate lyase from Fusarium moniliformae.
The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2-A resolution.
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.
Structure of a plant cell wall fragment complexed to pectate lyase C.
The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
Structure and function of pectic enzymes: virulence factors of plant pathogens.
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose.
Structure of pectate lyase A: comparison to other isoforms.
Identification of proline residues responsible for the slow folding kinetics in pectate lyase C by mutagenesis.
Folding kinetics of the protein pectate lyase C reveal fast-forming intermediates and slow proline isomerization.
Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis.
CASH--a beta-helix domain widespread among carbohydrate-binding proteins.
Characterization and implications of Ca2+ binding to pectate lyase C.
This enzyme is homologous to the counterpart enzyme (S00169), although one of the calcium binding residues, Asp184 (of 1jrg), is different from that (Glu166 of 1air) of its homologous enzyme. According to the literature [8], the catalytic reaction (beta-elimination) involves three process: (1) Neutralization of the carboxyl group adjacent to the deprotonation site of leaving group. (2) Deprotonation at the C-5 atom (deprotonation site of leaving group). (3) Protonation to the glycosidic oxygen (eliminated group). Although calcium ion usually plays a structural role, it is catalytically importnat in this enzyme. The calcium ion at the active site seems to acidify (or lower the pKa of) the alpha-proton at C-5 atom for abstraction by a general base, by polarizing and neutralizing the carboxy group (or uronic acid group) of the substrate (see [4], [5] & [6]). Here, the calcium ion acts as a Lewis acid. The literature [8] proposed that the conserved residue, Arg241 (of 1jrg), might serve as a general base, to abstract the proton at the C-5 atom. Although it is unusual for argnine residues to be a general base, the substrate carboxylate group (uronic acid) makes Arg241 to act as a general base, by lowering its pKa. As for the general acid, which protonates the glycosidic oxygen atom, a water molecule was suggested by the paper [8]. No alternative group has been found for this role. Moreover, during the catalysis, an enolic intermediate is formed and stabilized by Lys208 (of 1jrg) (see [8]).