Galactarolactone cycloisomerase

 

Experimentally characterized enzymes in the galactarolactone cycloisomerase (D-galactarolactone 3-deoxy-2-keto-L-threo-hexarate isomerase) family convert D-galactarolactone to 3-deoxy-2-keto-hexarate as part of D-galacturonate catabolism. The characterized enzyme from Agrobacterium tumefaciens is also active on D-glucarolactone.

 

Reference Protein and Structure

Sequence
A9CEQ8 UniProt (5.5.1.27) IPR034618 (Sequence Homologues) (PDB Homologues)
Biological species
Agrobacterium fabrum str. C58 (Bacteria) Uniprot
PDB
4hpn - Crystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops (1.6 Å) PDBe PDBsum 4hpn
Catalytic CATH Domains
3.20.20.120 CATHdb (see all for 4hpn)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:5.5.1.27)

D-galactaro-1,4-lactone(1-)
CHEBI:85317ChEBI
→
5-dehydro-4-deoxy-D-glucarate(2-)
CHEBI:42819ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: GCI,

Enzyme Mechanism

Introduction

Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. 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. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.

Catalytic Residues Roles

UniProt PDB* (4hpn)
Asp269 Asp269A Controls pKa of catalytic His269 modifies pKa
Glu246, Glu220, Asp194 Glu246A, Glu220A, Asp194A Forms the Mg(II) binding site. metal ligand
Lys166, His296, Glu329 Lys166A, His296A, Glu329A Acts as a general acid/base. 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

  1. Andberg M et al. (2012), J Biol Chem, 287, 17662-17671. Characterization of a novel Agrobacterium tumefaciens Galactarolactone Cycloisomerase Enzyme for Direct Conversion of D-Galactarolactone to 3-Deoxy-2-keto-L-threo-hexarate. DOI:10.1074/jbc.m111.335240. PMID:22493433.
  2. Vetting MW et al. (2016), Acta Crystallogr F Struct Biol Commun, 72, 36-41. Purification, crystallization and structural elucidation ofD-galactaro-1,4-lactone cycloisomerase fromAgrobacterium tumefaciensinvolved in pectin degradation. DOI:10.1107/s2053230x15023286. PMID:26750482.
  3. 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.

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Catalytic Residues Roles

Residue Roles
Asp269A modifies pKa
Asp194A metal ligand
Glu220A metal ligand
Glu246A metal ligand
His296A proton shuttle (general acid/base)
Glu329A proton shuttle (general acid/base)
Lys166A proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

Gemma L. Holliday