Ornithine decarboxylase
Catalyses the decarboxylation of ornithine to form putrescine. It belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domain superfamily (fold I)
Reference Protein and Structure
- Sequence
-
P43099
(4.1.1.17)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Lactobacillus sp. 30A (Bacteria)
- PDB
-
1ord
- CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION
(3.0 Å)
- Catalytic CATH Domains
-
3.40.640.10
(see all for 1ord)
- Cofactors
- Pyridoxal 5'-phosphate(2-) (1)
Enzyme Mechanism
Introduction
In this PLP-dependent reaction, lysine is displaced from the PLP cofactor by the substrate. The intermediate then undergoes double bond rearrangement and decarboxylation followed by a second transaldimination reaction in which the lysine displaces the product.
Catalytic Residues Roles
| UniProt | PDB* (1ord) | ||
| His224 | His223A | Holds the PLP ring in the correct orientation to avoid incorrect side reactions. Also helps stabilise reactive intermediates formed. | steric role, electrostatic stabiliser |
| Asp317 | Asp316A | Forms a hydrogen bond with the N atom of the PLP ring, helping to stabilise the reactive intermediates formed and activate the PLP cofactor to act as an electron sink. | electrostatic stabiliser |
| Lys356 | Lys355A | This lysine residue is covalently attached to PLP at the start of the reaction, is displaced by the amino acid substrate and subsequently acts as a general acid/base, before displacing the product from the PLP-cofactor to regenerate the active site. | covalent catalysis, 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
- Momany C et al. (1995), J Mol Biol, 252, 643-655. Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution. DOI:10.1006/jmbi.1995.0526. PMID:7563080.
- Momany C et al. (1995), Protein Sci, 4, 849-854. Structural motifs for pyridoxal-5'-phosphate binding in decarboxylases: an analysis based on the crystal structure of the Lactobacillus 30a ornithine decarboxylase. DOI:10.1002/pro.5560040504. PMID:7663340.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Lys355A | covalent catalysis, proton shuttle (general acid/base) |
| Asp316A | electrostatic stabiliser |
| His223A | steric role, electrostatic stabiliser |