L-fuconate dehydratase

 

L-fuconate dehydratase is a member of the enolase superfamily and is known to play a role in the catabolism of L-fucose. It catalyses the dehydration of L-fuconate to 2-keto-3-deoxy-L-fuconate by the abstraction of the proton alpha to the carboxylate group of the substrate to generate an enediolate intermediate that is stabilised by an essential magnesium ion.

 

Reference Protein and Structure

Sequence
Q8P3K2 UniProt (4.2.1.68) IPR034610 (Sequence Homologues) (PDB Homologues)
Biological species
Xanthomonas campestris pv. campestris str. ATCC 33913 (Bacteria) Uniprot
PDB
2hxt - Crystal structure of L-Fuconate Dehydratase from Xanthomonas campestris liganded with Mg++ and D-erythronohydroxamate (1.7 Å) PDBe PDBsum 2hxt
Catalytic CATH Domains
3.20.20.120 CATHdb (see all for 2hxt)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.68)

L-fuconate
CHEBI:21291ChEBI
→
2-dehydro-3-deoxy-L-fuconate
CHEBI:37448ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: L-fuconate hydro-lyase,

Enzyme Mechanism

Introduction

This enzyme follows the classical enolase superfamily mechanism in which Lys220 abstracts proton from the carbon alpha to the carboxylate group. A beta elimination then occurs to produce water and deprotonated His351. The intermediate then undergoes a keto-enol tautomerisation assisted by His351 and to generate the final product and Lys220.

Catalytic Residues Roles

UniProt PDB* (2hxt)
His351 His351A Acts as a general acid/base. This residue is responsible for the donation of a proton to the leaving water molecule. proton acceptor, proton donor
Asp324 Asp324A Modifies the pKa of the catalytic histidine residue. metal ligand
Lys220 Lys220A Acts as a general acid/base. This is the residue responsible for the initial alpha proton abstraction. proton acceptor, proton donor
Glu301, Asp248, Glu274 Glu301A, Asp248A, Glu274A Forms part of the magnesium binding site. metal ligand
*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

proton transfer, overall product formed, assisted keto-enol tautomerisation, dehydration, unimolecular elimination by the conjugate base, native state of enzyme regenerated

References

  1. Yew WS et al. (2006), Biochemistry, 45, 14582-14597. Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. DOI:10.1021/bi061687o. PMID:17144652.

Step 1. Lys220 abstracts the proton alpha to the carboxylate group.

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Catalytic Residues Roles

Residue Roles
Asp324A metal ligand
Glu274A metal ligand
Glu301A metal ligand
Asp248A modifies pKa
Lys220A proton acceptor

Chemical Components

proton transfer, overall product formed, assisted keto-enol tautomerisation

Step 2. A beta elimination produces water with concomitant deprotonation of His351.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp324A metal ligand
Glu274A metal ligand
Glu301A metal ligand
Asp248A modifies pKa
His351A proton donor

Chemical Components

dehydration, overall product formed, ingold: unimolecular elimination by the conjugate base, proton transfer

Step 3. His351 abstracts a proton from the intermediate OH group on the carbon alpha to the carboxylate in an assisted keto-enol tautomerisation with concomitant deprotonation of Lys220.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp324A metal ligand
Glu274A metal ligand
Glu301A metal ligand
Asp248A modifies pKa
Lys220A proton donor
His351A proton acceptor

Chemical Components

assisted keto-enol tautomerisation, native state of enzyme regenerated, proton transfer, overall product formed
Download: Image, Marvin File

Step 1. Lys220 abstracts the proton alpha to the carboxylate group.

Step 2. A beta elimination produces water with concomitant deprotonation of His351.

Step 3. His351 abstracts a proton from the intermediate OH group on the carbon alpha to the carboxylate in an assisted keto-enol tautomerisation with concomitant deprotonation of Lys220.

Products.

Contributors

Gemma L. Holliday