Galactarate dehydratase (type III)

 

Characterized enzymes in the galactarate dehydratase III family catalyse the dehydration of m-galactarate to 2-keto-3-deoxy-galactarate, as part of the synthesis of alpha-ketoglutarate. They differ from previously characterised galactarate dehydratases in the enolase superfamily, utilising some unique catalytic residues. The characterised enzyme from Agrobacterium tumefaciens C58 has also been shown to convert D-galacturonate to 3-deoxy-D-xylo-hexarate or 3-deoxy-D-lyxo-hexarate, an unexpected reaction for an enolase superfamily member, as it involves abstraction of a proton alpha to an aldehyde group rather than a proton alpha to a carboxylate group.

 

Reference Protein and Structure

Sequence
B9JNP7 UniProt IPR034623 (Sequence Homologues) (PDB Homologues)
Biological species
Agrobacterium radiobacter K84 (Bacteria) Uniprot
PDB
4jn7 - CRYSTAL STRUCTURE OF AN ENOLASE (PUTATIVE GALACTARATE DEHYDRATASE, TARGET EFI-500740) FROM AGROBACTERIUM RADIOBACTER, BOUND NA and L-MALATE, ORDERED ACTIVE SITE (1.15 Å) PDBe PDBsum 4jn7
Catalytic CATH Domains
3.20.20.120 CATHdb (see all for 4jn7)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.158)

galactarate(2-)
CHEBI:16537ChEBI
→
3-deoxy-D-threo-hex-2-ulosarate(2-)
CHEBI:78267ChEBI
+
water
CHEBI:15377ChEBI

Enzyme Mechanism

Introduction

Proton abstraction is performed by His 292 followed by general acid-catalysed dehydration by His 191. H292 then facilitates tautomerisation to the final product, 2-keto-3-deoxy-galactarate.

Catalytic Residues Roles

UniProt PDB* (4jn7)
His292, His191 His292A, His191A Act as a general acid/base. proton shuttle (general acid/base)
Glu242, Asp189, Glu216 Glu242A, Asp189A, Glu216A Forms part of the magnesium binding site. metal ligand
Asp265 Asp265A Controls pKa of His292 that functions as general base. modifies pKa
*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. Groninger-Poe FP et al. (2014), Biochemistry, 53, 4192-4203. Evolution of Enzymatic Activities in the Enolase Superfamily: Galactarate Dehydratase III fromAgrobacterium tumefaciensC58. DOI:10.1021/bi5005377. PMID:24926996.

Step 1.

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Catalytic Residues Roles

Residue Roles
Asp189A metal ligand
Glu216A metal ligand
Glu242A metal ligand
Asp265A modifies pKa
His191A proton shuttle (general acid/base)
His292A proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Shoshana Brown