Pectate lyase
Pectate lyase from Azospirillum irakense (PelA) catalyses the degradation of pectin. Pectate lyases (also known as pectate transeliminases) are secreted microbial enzymes that degrade pectin, and are therefore important in plant pathogenesis.
Reference Protein and Structure
- Sequence
-
Q9X592
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Niveispirillum irakense (Bacteria)
- PDB
-
1r76
- Structure of a pectate lyase from Azospirillum irakense
(2.65 Å)
- Catalytic CATH Domains
-
1.50.10.20
(see all for 1r76)
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
Arg 307 deprotonates the C5 H atom from the axial position. The negative charge is stabilised on the carboxyl oxygen atom by Asn 172. The carboxyl group is reformed with the elimination of the leaving group from the C4 position. The leaving group is protonated to form an alcohol, most likey by the previously protonated Arg 307.
Catalytic Residues Roles
| UniProt | PDB* (1r76) | ||
| Asn172 | Asn172(148)A | Stabilises the negative charge on the intermediate. | electrostatic stabiliser |
| Arg307 | Arg307(283)A | Deprotonates the C5 atom of pectin. Also is the most likely candidate for protonation of the leaving group. | 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
- Novoa De Armas H et al. (2004), Acta Crystallogr D Biol Crystallogr, 60, 999-1007. Azospirillum irakensepectate lyase displays a toroidal fold. DOI:10.1107/s090744490400602x. PMID:15159558.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asn172(148)A | electrostatic stabiliser |
| Arg307(283)A | proton shuttle (general acid/base) |