Pectate lyase C (polysaccharide lyase 1 family)
Involved in maceration and soft-rotting of plant tissue. Pectate lyase catalyses the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
Reference Protein and Structure
- Sequence
-
P11073
(4.2.2.2)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Dickeya chrysanthemi (Bacteria)
- PDB
-
2pec
- THE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT 2.2 ANGSTROMS RESOLUTION: IMPLICATIONS FOR AN ENZYMATIC MECHANISM
(2.2 Å)
- Catalytic CATH Domains
-
2.160.20.10
(see all for 2pec)
- Cofactors
- Calcium(2+) (1)
Enzyme Reaction (EC:4.2.2.2)
→
+
Alternative enzyme names: Alpha-1,4-D-endopolygalacturonic acid lyase, PGA lyase, PPase-N, Polygalacturonic acid trans-eliminase, Endo-alpha-1,4-polygalacturonic acid lyase, Endogalacturonate transeliminase, Endopectin methyltranseliminase, Pectate transeliminase, Pectic acid lyase, Pectic acid transeliminase, Pectic lyase, Pectin trans-eliminase, Polygalacturonate lyase, Polygalacturonic acid lyase, Polygalacturonic transeliminase,
Enzyme Mechanism
Introduction
The reaction proceeds via a beta-elimination reaction in which the highly conserved Arg218 (activated by Ca(II)) acts as a general acid/base.
Catalytic Residues Roles
| UniProt | PDB* (2pec) | ||
| Glu188, Asp192, Asp151, Asp153 | Glu166A, Asp170A, Asp129A, Asp131A | Forms part of the Ca(II) binding site. | metal ligand |
| Arg240 | Arg218A | Acts as a general acid/base. | modifies pKa, proton shuttle (general acid/base) |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Herron SR et al. (2000), Proc Natl Acad Sci U S A, 97, 8762-8769. Structure and function of pectic enzymes: Virulence factors of plant pathogens. DOI:10.1073/pnas.97.16.8762. PMID:10922032.
- Herron SR et al. (2003), J Biol Chem, 278, 12271-12277. Characterization and implications of Ca2+ binding to pectate lyase C. DOI:10.1074/jbc.M209306200. PMID:12540845.
- Yoder MD et al. (1995), Plant Physiol, 107, 349-364. The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism). DOI:10.1104/pp.107.2.349.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Arg218A | proton shuttle (general acid/base) |
| Asp129A | metal ligand |
| Asp131A | metal ligand |
| Glu166A | metal ligand |
| Asp170A | metal ligand |
| Arg218A | modifies pKa |