Isochorismatase
Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems. Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria.
Reference Protein and Structure
- Sequence
-
P0DPB9
(3.3.2.15)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Pseudomonas aeruginosa PAO1 (Bacteria)
- PDB
-
1nf9
- Crystal Structure of PhzD protein from Pseudomonas aeruginosa
(1.5 Å)
- Catalytic CATH Domains
-
3.40.50.850
(see all for 1nf9)
Enzyme Reaction (EC:3.3.2.1)
+
→
+
Alternative enzyme names: 2,3-dihydro-2,3-dihydroxybenzoate synthase, 2,3-dihydroxy-2,3-dihydrobenzoate synthase, 2,3-dihydroxy-2,3-dihydrobenzoic synthase,
Enzyme Mechanism
Introduction
The carboxylate of Asp38 acts as a general acid to protonate the substrate, yielding a carbocation/oxocarbonium ion that is then rapidly hydrated to form a hemiketal intermediate, which then decomposes spontaneously to products.
Catalytic Residues Roles
| UniProt | PDB* (1nf9) | ||
| Asp38 | Asp38A | D38 acts as a general acid in the initial protonation of the substrate in what is probably the slowest chemical step. The resulting carboxylate may further act to stabilize the transiently formed carbocation/oxocarbonium ion. | proton shuttle (general acid/base), electrostatic stabiliser |
| His37 | His37A | Proposed to be involved in stabilising and correctly positioning the K122 and D38. | electrostatic stabiliser, steric role |
| Lys122 | Lys122A | Proposed to act as the general acid/base involved in activating the nucleophilic water molecule. | 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
- Parsons JF et al. (2003), Biochemistry, 42, 5684-5693. Structure and Mechanism ofPseudomonas aeruginosaPhzD, an Isochorismatase from the Phenazine Biosynthetic Pathway†,‡,§. DOI:10.1021/bi027385d. PMID:12741825.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp38A | proton shuttle (general acid/base), electrostatic stabiliser |
| Lys122A | proton shuttle (general acid/base) |
| His37A | electrostatic stabiliser, steric role |