Tryptophanase
Tryptophan indole-lyase (also known as tryptophanase or Trpase) is a pyridoxal 5'-phosphate (PLP) dependent enzyme that catalyses the reversible beta-elimination reaction of L-Tryptophan to form indole and ammonium pyruvate. The enzyme has been found in a wide variety of Gram-negative bacteria.
Reference Protein and Structure
- Sequence
-
P28796
(4.1.99.1)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Proteus vulgaris (Bacteria)
- PDB
-
1ax4
- TRYPTOPHANASE FROM PROTEUS VULGARIS
(2.1 Å)
- Catalytic CATH Domains
-
3.40.640.10
3.90.1150.10
(see all for 1ax4)
- Cofactors
- Pyridoxal 5'-phosphate(2-) (1)
Enzyme Reaction (EC:4.1.99.1)
Enzyme Mechanism
Introduction
The catalytic cycle of tryptophanase consists of the following steps: (1) Association of the amino acid substrate with the enzyme to form the Michaelis complex; (2) Formation of the external aldimine (transaldimination); (3) Quinonoid formation by alpha-proton abstraction from the external aldimine; (4) Tautomerisation of the indolyl group; (5) Elimination of indole and formation of the aminoacrylate Schiff base intermediate; (6) Restoration of the internal aldimine (transaldimination); (7) Release of aminoacrylate and decomposition to pyruvate and ammonia.
Catalytic Residues Roles
| UniProt | PDB* (1ax4) | ||
| Tyr72 | Tyr72B | General acid/base, directly transfers a proton to the indole side group to assist with tautomerisation. | proton shuttle (general acid/base) |
| Asp223 | Asp223A | Stabilises the PLP-intermediates. | electrostatic stabiliser |
| His458 | His458A | Forms a hydrogen bond with the carboxylate anion of Asp133 to stabilise the negative charge in hydrophobic conditions. | activator, electrostatic stabiliser |
| Asp133 | Asp133A | General acid/base to remove the proton from the NH group of indole. | proton shuttle (general acid/base), electrostatic stabiliser |
| Lys266 (ptm) | Llp266A (ptm) | Initially bound to the PLP cofactor, acts as a general acid/base during the course of the reaction and also the catalytic nucleophile in the product release steps. | covalent catalysis, proton shuttle (general acid/base) |
| Phe132, Ala225 | Phe132A, Ala225A | Involved in holding the free-PLP in the correct orientation. | steric role |
Chemical Components
References
- Demidkina TV et al. (2009), Mol Biol (Mosk), 43, 269-283. Spatial structure and the mechanism of tyrosine phenol-lyase and tryptophan indole-lyase. DOI:10.1134/s0026893309020101. PMID:19425498.
- Faleev NG et al. (2014), Biochim Biophys Acta, 1844, 1860-1867. A straightforward kinetic evidence for coexistence of “induced fit” and “selected fit” in the reaction mechanism of a mutant tryptophan indole lyase Y72F from Proteus vulgaris. DOI:10.1016/j.bbapap.2014.07.014. PMID:25084024.
- Kulikova VV et al. (2006), Biochim Biophys Acta, 1764, 750-757. Tryptophanase from Proteus vulgaris: The conformational rearrangement in the active site, induced by the mutation of Tyrosine 72 to Phenylalanine, and its mechanistic consequences. DOI:10.1016/j.bbapap.2005.12.003. PMID:16455316.
- Phillips RS et al. (2003), Biochim Biophys Acta Proteins Proteomics, 1647, 167-172. Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase. DOI:10.1016/s1570-9639(03)00089-x.
- Isupov MN et al. (1998), J Mol Biol, 276, 603-623. Crystal structure of tryptophanase. DOI:10.1006/jmbi.1997.1561. PMID:9551100.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr72B | proton shuttle (general acid/base) |
| Llp266A (ptm) | proton shuttle (general acid/base), covalent catalysis |
| Asp223A | electrostatic stabiliser |
| Phe132A | steric role |
| Asp133A | electrostatic stabiliser, proton shuttle (general acid/base) |
| Ala225A | steric role |
| His458A | electrostatic stabiliser, activator |