D-galactarolactone isomerase

 

Catalyses the isomerisation of D-galactaro-1,5-lactone to D-galactaro-1,4-lactone. This is a step in the oxidative degradation pathway of D-galacturonate, which allows Agrobacterium tumefaciens to utilise D-galacturonate as a sole carbon source. This enzyme belongs to the amidohydrolase superfamily. Unlike many members of the amidohydrolase superfamily, this protein does not require a divalent metal for its lactonase activity

 

Reference Protein and Structure

Sequence
A9CEQ7 UniProt (5.4.1.4) IPR006680 (Sequence Homologues) (PDB Homologues)
Biological species
Agrobacterium fabrum str. C58 (Bacteria) Uniprot
PDB
4mup - Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI target 505157), apo structure (1.6 Å) PDBe PDBsum 4mup
Catalytic CATH Domains
3.20.20.140 CATHdb (see all for 4mup)
Click To Show Structure

Enzyme Reaction (EC:5.4.1.4)

D-galactaro-1,5-lactone(1-)
CHEBI:83383ChEBI
→
D-galactaro-1,4-lactone(1-)
CHEBI:85317ChEBI
Alternative enzyme names: GLI,

Enzyme Mechanism

Introduction

The substrate undergoes auto-catalytic formation of the oxygen bridge, activated by Asn240. The formed oxyanion then collapses to form the five membered ring. The modest rate enhancement over the non-enzymatic reaction is thought to come from the preferential binding of the boat conformer of the delta-lactone ring to enforce the proximity of the 4-OH group and the lactone carbonyl group.

Catalytic Residues Roles

UniProt PDB* (4mup)
Asn240 Asn240(260)A This residue is the equivalent of the conserved aspartate in other amidohydrolase proteins; it is likely to stabilise and activate the substrate for auto-catalysis. enhance reactivity, 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

cyclisation, overall reactant used, intramolecular nucleophilic addition, overall product formed, intramolecular elimination, decyclisation

References

  1. Bouvier JT et al. (2014), Biochemistry, 53, 614-616. Galactaro δ-Lactone Isomerase: Lactone Isomerization by a Member of the Amidohydrolase Superfamily. DOI:10.1021/bi5000492. PMID:24450804.

Step 1. The hydroxyl group opposite the lactone carbonyl initiates a nucleophilic attack to form the cyclic intermediate.

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Catalytic Residues Roles

Residue Roles
Asn240(260)A enhance reactivity

Chemical Components

cyclisation, overall reactant used, ingold: intramolecular nucleophilic addition

Step 2. The oxyanion collapses to form the 5-membered ring with deprotonation of the bridging oxygen.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asn240(260)A electrostatic stabiliser

Chemical Components

overall product formed, ingold: intramolecular elimination, decyclisation
Download: Image, Marvin File

Step 1. The hydroxyl group opposite the lactone carbonyl initiates a nucleophilic attack to form the cyclic intermediate.

Step 2. The oxyanion collapses to form the 5-membered ring with deprotonation of the bridging oxygen.

Products.

Contributors

Gemma L. Holliday