Prephenate dehydratase

 

Prephenate dehydratase (EC:4.2.1.51, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria, e.g. E. coli PDT is part of the multi-functional P-protein that also catalyses the transformation of chorismate into prephenate (chorismate mutase), while in other bacteria it is a monofunctional enzyme.

 

Reference Protein and Structure

Sequence
Q8KBW6 UniProt (4.2.1.51) IPR001086 (Sequence Homologues) (PDB Homologues)
Biological species
Chlorobium tepidum TLS (Bacteria) Uniprot
PDB
2qmx - The crystal structure of L-Phe inhibited prephenate dehydratase from Chlorobium tepidum TLS (2.3 Å) PDBe PDBsum 2qmx
Catalytic CATH Domains
3.40.190.10 CATHdb (see all for 2qmx)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.51)

hydron
CHEBI:15378ChEBI
+
(1s,4s)-prephenate(2-)
CHEBI:29934ChEBI
→
keto-phenylpyruvate
CHEBI:18005ChEBI
+
water
CHEBI:15377ChEBI
+
carbon dioxide
CHEBI:16526ChEBI
Alternative enzyme names: Prephenate hydro-lyase (decarboxylating),

Enzyme Mechanism

Introduction

The decarboxylation and dehydration reactions occur in a concerted manner. The carboxylate group initiates the reaction, causing aromatisation of the ring and elimination of the hydroxide group, which abstracts a proton from Thr171. It is thought that the driving force for this reaction is the aromatisation of the substrate, but it is not clear if the pKa of the active site threonine is sufficiently modified for it to be a good proton donor. However, it is the only residue close enough in the crystal structure to be the proton donor.

Catalytic Residues Roles

UniProt PDB* (2qmx)
Thr171 Thr171(174)A Part of the highly conserved TRF motif, thought to act as the proton donor for the hydrolysis reaction. proton acceptor, proton donor
Phe173 Phe173(176)A Helps stabilise the transition state. electrostatic stabiliser
*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

decarboxylation, dehydration, intramolecular elimination, inferred reaction step, native state of enzyme regenerated, proton transfer

References

  1. Van Vleet J et al. (2010), Biochim Biophys Acta, 1804, 752-754. 13C isotope effect on the reaction catalyzed by prephenate dehydratase. DOI:10.1016/j.bbapap.2009.11.018. PMID:19948253.
  2. Shin MH et al. (2014), J Microbiol, 52, 490-495. X-ray structure of prephenate dehydratase from Streptococcus mutans. DOI:10.1007/s12275-014-3645-8. PMID:24610334.
  3. Tan K et al. (2008), J Struct Biol, 162, 94-107. Structures of open (R) and close (T) states of prephenate dehydratase (PDT)—Implication of allosteric regulation by l-phenylalanine. DOI:10.1016/j.jsb.2007.11.009. PMID:18171624.
  4. Hsu SK et al. (2004), Arch Microbiol, 181, 237-244. Mutational analysis of feedback inhibition and catalytic sites of prephenate dehydratase from Corynebacterium glutamicum. DOI:10.1007/s00203-004-0649-5. PMID:14749915.

Step 1. The carboxylate group initiates the reaction, resulting in the re-aromatisation of the substrate and elimination of the water molecule, with concomitant deprotonation of Thr171.

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Catalytic Residues Roles

Residue Roles
Phe173(176)A electrostatic stabiliser
Thr171(174)A proton donor

Chemical Components

decarboxylation, dehydration, ingold: intramolecular elimination

Step 2. Inferred return step to regenerate the active site threonine residue.

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Catalytic Residues Roles

Residue Roles
Thr171(174)A proton acceptor

Chemical Components

inferred reaction step, native state of enzyme regenerated, proton transfer
Download: Image, Marvin File

Step 1. The carboxylate group initiates the reaction, resulting in the re-aromatisation of the substrate and elimination of the water molecule, with concomitant deprotonation of Thr171.

Step 2. Inferred return step to regenerate the active site threonine residue.

Products.

Contributors

Jonathan T. W. Ng, Gemma L. Holliday